Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xaq Working: n-0-39.cluster.ucsf.bkslab.org:/scratch/xiaobo/25650/xaq-8058115.17 Result: /scratch/xiaobo/25650/xaq-8058115.17 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xaq 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/xaq mkdir: created directory `/scratch/xiaobo/25650' mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17' /scratch/xiaobo/25650/xaq-8058115.17 /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/25650/xaq-8058115.17/working' mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/protonate' Storing results in /scratch/xiaobo/25650/xaq-8058115.17/finished Working in /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 /scratch/xiaobo/25650/xaq-8058115.17/working/protonate /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Using inputs as protomers/tautomers. No processing done 470 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/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Bulk generating 3D conformations all protomers in /scratch/xiaobo/25650/xaq-8058115.17/working/3D mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/25650/xaq-8058115.17/working/protonate/xaq-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 ZINC000180862534 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building' mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862534 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/1 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/2 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/3 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/3' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/4 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/4' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862534 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/finished' Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 Building ZINC000180862534 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862534 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 1) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 2) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 3) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 4) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862534 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 Building ZINC000180862534 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862534 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 1) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 2) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 3) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 4) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862534 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 Building ZINC000180862534 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862534 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 1) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 2) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 3) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 4) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862534 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 12, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862534 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862534 Building ZINC000180862550 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862550 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/5 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/6 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/7 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/7' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/8 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/8' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862550 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 Building ZINC000180862550 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862550 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 5) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 6) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 7) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 8) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862550 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 Building ZINC000180862550 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862550 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 5) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 6) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 7) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 8) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862550 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 Building ZINC000180862550 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180862550 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 5) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 6) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 9, 9, 10, 43, 43, 43, 43, 43, 43, 45, 45, 45, 43, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 9, 43, 43, 43, 43, 43, 43, 45, 45, 45, 45, 45, 45, 45, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 7) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 8) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)C2)cc1) `ZINC000180862550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180862550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000180862550 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H]2CCCN(C3CCC3)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', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 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] 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] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180862550 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180862550 Building ZINC000180883980 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180883980 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/9 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)cc1) `ZINC000180883980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180883980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000180883980 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 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, 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/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/10 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)cc1) `ZINC000180883980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180883980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000180883980 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 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, 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/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180883980 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 Building ZINC000180883980 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180883980 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 9) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)cc1) `ZINC000180883980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180883980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000180883980 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 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, 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/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 10) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)cc1) `ZINC000180883980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180883980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000180883980 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(c3ccccc3)nc2C)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 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, 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/25650/xaq-8058115.17/working/building/ZINC000180883980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180883980 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180883980 Building ZINC000181004630 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181004630 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/11 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1) `ZINC000181004630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181004630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181004630 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 4, 4, 7, 16, 22, 22, 20, 22, 22, 7, 11, 22, 22, 22, 5, 5, 5, 5, 5, 5, 5, 16, 16, 22, 22, 22, 22, 22, 11, 11, 22, 22, 22, 22, 22, 22, 66, 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: 245 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/12 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1) `ZINC000181004630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181004630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181004630 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 4, 4, 7, 17, 23, 23, 19, 23, 23, 7, 12, 22, 22, 22, 5, 5, 5, 5, 5, 5, 5, 17, 17, 23, 23, 23, 23, 23, 12, 12, 22, 22, 22, 22, 22, 22, 66, 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: 255 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181004630 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 Building ZINC000181004630 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181004630 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 11) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1) `ZINC000181004630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181004630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181004630 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 4, 4, 7, 16, 22, 22, 20, 22, 22, 7, 11, 22, 22, 22, 5, 5, 5, 5, 5, 5, 5, 16, 16, 22, 22, 22, 22, 22, 11, 11, 22, 22, 22, 22, 22, 22, 66, 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: 245 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 12) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1) `ZINC000181004630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181004630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181004630 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)CC(C)(C)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 4, 4, 7, 17, 23, 23, 19, 23, 23, 7, 12, 22, 22, 22, 5, 5, 5, 5, 5, 5, 5, 17, 17, 23, 23, 23, 23, 23, 12, 12, 22, 22, 22, 22, 22, 22, 66, 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: 255 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181004630 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181004630 Building ZINC000181007439 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181007439 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/13 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(C)C)nc2)cc1) `ZINC000181007439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181007439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181007439 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(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.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 24, 24, 24, 24, 45, 50, 50, 50, 24, 24, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/14 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(C)C)nc2)cc1) `ZINC000181007439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181007439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181007439 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(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.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 26, 26, 26, 26, 48, 50, 50, 50, 26, 26, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181007439 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 Building ZINC000181007439 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181007439 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 13) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(C)C)nc2)cc1) `ZINC000181007439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181007439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181007439 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(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.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 24, 24, 24, 24, 45, 50, 50, 50, 24, 24, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 14) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(C)C)nc2)cc1) `ZINC000181007439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181007439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000181007439 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(OC(C)(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.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 26, 26, 26, 26, 48, 50, 50, 50, 26, 26, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181007439 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181007439 Building ZINC000181031512 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031512 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/15 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/15' -> `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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/16 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/16' -> `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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/17 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/17' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/18 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/18' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031512 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 Building ZINC000181031512 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031512 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 15) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 16) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 17) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 18) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031512 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 Building ZINC000181031512 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031512 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 15) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 16) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 17) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 18) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031512 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 Building ZINC000181031512 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031512 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 15) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 16) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 18, 22, 22, 36, 49, 49, 40, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 18, 18, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 17) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 18) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031512.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031512 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 18, 21, 21, 32, 48, 48, 47, 48, 48, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 8, 18, 18, 21, 21, 21, 32, 32, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031512 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031512 Building ZINC000181031531 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031531 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/19 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/19' -> `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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/20 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/20' -> `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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/21 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/21' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/22 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/22' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031531 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 Building ZINC000181031531 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031531 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 19) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 20) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 21) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 22) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031531 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 Building ZINC000181031531 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031531 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 19) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 20) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 21) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 22) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031531 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 Building ZINC000181031531 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000181031531 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 19) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 20) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 23, 24, 24, 29, 42, 42, 29, 42, 42, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 23, 23, 24, 24, 24, 29, 29, 42, 42, 29, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 21) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 22) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)CN(C)Cc2ccccc2)cc1) `ZINC000181031531.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000181031531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181031531 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)CN(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', 'H', 'C.3', '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, 7, 5, 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, 9, 9, 19, 23, 23, 37, 49, 49, 38, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 9, 19, 19, 23, 23, 23, 37, 37, 49, 49, 37, 49, 49, 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: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181031531 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181031531 Building ZINC000177743033 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177743033 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/23 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000177743033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177743033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177743033 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 11, 3, 11, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 9, 9, 23, 23, 23, 23, 23, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/24 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000177743033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177743033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177743033 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 11, 3, 11, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 11, 21, 21, 21, 21, 21, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000177743033 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 Building ZINC000177743033 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177743033 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 23) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000177743033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177743033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177743033 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 11, 3, 11, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 9, 9, 23, 23, 23, 23, 23, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 24) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1) `ZINC000177743033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177743033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177743033 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCC1 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.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 11, 3, 11, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 11, 21, 21, 21, 21, 21, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000177743033 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177743033 Building ZINC000181241134 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181241134 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/25 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)cc1) `ZINC000181241134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181241134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181241134 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)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', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 8, 1, 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] 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, 33, 33, 33, 33, 33, 33, 50, 50, 49, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 33, 33, 33, 33, 50, 50, 33, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/26 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)cc1) `ZINC000181241134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181241134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181241134 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)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', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 8, 1, 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] 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 33, 33, 33, 50, 50, 48, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 33, 33, 33, 33, 50, 50, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181241134 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 Building ZINC000181241134 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181241134 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 25) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)cc1) `ZINC000181241134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181241134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181241134 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)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', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 8, 1, 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] 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, 33, 33, 33, 33, 33, 33, 50, 50, 49, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 33, 33, 33, 33, 50, 50, 33, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 26) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)cc1) `ZINC000181241134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181241134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181241134 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn(C)nc2c2ccccc2)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', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 5, 8, 1, 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] 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 33, 33, 33, 33, 33, 33, 50, 50, 48, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 33, 33, 33, 33, 50, 50, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181241134 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181241134 Building ZINC000181446819 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181446819 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/27 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)c2)cc1) `ZINC000181446819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181446819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181446819 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)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', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 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] 0 hydrogens need 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, 7, 7, 25, 45, 45, 45, 25, 25, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 25, 25, 45, 45, 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: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/28 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)c2)cc1) `ZINC000181446819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181446819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181446819 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)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', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 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] 0 hydrogens need 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, 7, 7, 24, 44, 44, 44, 30, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 24, 24, 44, 44, 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: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181446819 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 Building ZINC000181446819 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181446819 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 27) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)c2)cc1) `ZINC000181446819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181446819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181446819 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)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', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 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] 0 hydrogens need 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, 7, 7, 25, 45, 45, 45, 25, 25, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 25, 25, 45, 45, 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: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 28) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)c2)cc1) `ZINC000181446819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181446819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000181446819 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(F)c(F)c(F)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', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 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] 0 hydrogens need 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, 7, 7, 24, 44, 44, 44, 30, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 24, 24, 44, 44, 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: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181446819 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181446819 Building ZINC000182218318 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182218318 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/29 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C) `ZINC000182218318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182218318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218318 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 37 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/30 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C) `ZINC000182218318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182218318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218318 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182218318 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 Building ZINC000182218318 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182218318 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 29) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C) `ZINC000182218318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182218318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218318 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 37 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 30) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C) `ZINC000182218318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182218318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218318 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 38 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182218318 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218318 Building ZINC000182218352 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182218352 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/31 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182218352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 37, 37, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/32 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182218352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 37, 37, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182218352 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 Building ZINC000182218352 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182218352 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 31) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182218352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218352 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 37, 37, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 32) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182218352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218352 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 37, 37, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182218352 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218352 Building ZINC000182218367 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182218367 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/33 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182218367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218367 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 36 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/34 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182218367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218367 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 41 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182218367 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 Building ZINC000182218367 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182218367 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 33) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182218367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218367 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 36 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 34) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C) `ZINC000182218367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182218367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000182218367 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cc(C)ccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 41 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182218367 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182218367 Building ZINC000182286585 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182286585 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/35 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1) `ZINC000182286585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182286585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182286585 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 9, 9, 21, 49, 49, 49, 49, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 9, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/36 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1) `ZINC000182286585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182286585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182286585 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 9, 9, 20, 49, 49, 49, 49, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 9, 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182286585 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 Building ZINC000182286585 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182286585 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 35) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1) `ZINC000182286585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182286585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182286585 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 9, 9, 21, 49, 49, 49, 49, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 9, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 36) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1) `ZINC000182286585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182286585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182286585 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C3CCCC3)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 4, 9, 9, 20, 49, 49, 49, 49, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 9, 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: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182286585 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182286585 Building ZINC000182428330 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182428330 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/37 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182428330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428330 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9] 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, 39, 40, 41, 42]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/38 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182428330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428330 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 4, 4, 4, 4, 14, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 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, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182428330 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 Building ZINC000182428330 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182428330 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 37) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182428330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428330 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9] 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, 39, 40, 41, 42]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 38) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182428330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428330 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 4, 4, 4, 4, 14, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 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, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182428330 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428330 Building ZINC000182428348 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182428348 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/39 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182428348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428348 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 4, 4, 4, 4, 14, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 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, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/40 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182428348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428348 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 15, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9] 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, 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/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182428348 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 Building ZINC000182428348 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182428348 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 39) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182428348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428348 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 4, 4, 4, 4, 14, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 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, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 40) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)C2)cc1) `ZINC000182428348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182428348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182428348 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Oc3cccc(F)c3)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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 15, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50, 4, 4, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9] 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, 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/25650/xaq-8058115.17/working/building/ZINC000182428348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182428348 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182428348 Building ZINC000182432732 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182432732 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/41 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000182432732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182432732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182432732 none O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[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.2', 'O.2', 'N.am', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 6, 1, 8, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 6, 6, 6, 10, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/42 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000182432732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182432732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182432732 none O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[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.2', 'O.2', 'N.am', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 6, 1, 8, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182432732 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 Building ZINC000182432732 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182432732 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 41) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000182432732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182432732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182432732 none O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[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.2', 'O.2', 'N.am', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 6, 1, 8, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 6, 6, 6, 10, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 42) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000182432732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182432732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000182432732 none O=C(Nc1cc2c(=O)[nH]cnc2cc1F)[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.2', 'O.2', 'N.am', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 6, 1, 8, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182432732 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182432732 Building ZINC000182443028 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182443028 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/43 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCNc2cccc(F)c2)cc1) `ZINC000182443028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182443028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182443028 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCNc2cccc(F)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 15, 21, 25, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 17, 17, 21, 21, 25, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/44 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCCNc2cccc(F)c2)cc1) `ZINC000182443028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182443028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182443028 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCNc2cccc(F)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 14, 20, 24, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 16, 16, 20, 20, 24, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182443028 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 Building ZINC000182443028 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182443028 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 43) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCCCNc2cccc(F)c2)cc1) `ZINC000182443028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182443028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182443028 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCCNc2cccc(F)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 15, 21, 25, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 17, 17, 21, 21, 25, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 44) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCCCNc2cccc(F)c2)cc1) `ZINC000182443028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182443028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000182443028 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCCNc2cccc(F)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 14, 20, 24, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 16, 16, 20, 20, 24, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182443028 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182443028 Building ZINC000177844725 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177844725 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/45 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000177844725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177844725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177844725 none CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 34, 26, 8, 26, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/46 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000177844725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177844725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177844725 none CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 24, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000177844725 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 Building ZINC000177844725 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177844725 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 45) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000177844725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177844725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177844725 none CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 34, 26, 8, 26, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 46) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000177844725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177844725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000177844725 none CC(C)(C)OC(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 24, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000177844725 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000177844725 Building ZINC000183077857 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183077857 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/47 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)cc3c2OCC3)cc1) `ZINC000183077857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183077857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183077857 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)cc3c2OCC3)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 1, 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, 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, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 45, 45, 45, 45, 45, 45, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/48 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)cc3c2OCC3)cc1) `ZINC000183077857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183077857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183077857 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)cc3c2OCC3)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 1, 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, 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, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 43, 43, 43, 43, 43, 43, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183077857 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 Building ZINC000183077857 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183077857 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 47) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCc2cc(Cl)cc3c2OCC3)cc1) `ZINC000183077857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183077857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183077857 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Cl)cc3c2OCC3)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 1, 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, 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, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 45, 45, 45, 45, 45, 45, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 48) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCc2cc(Cl)cc3c2OCC3)cc1) `ZINC000183077857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183077857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183077857 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Cl)cc3c2OCC3)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 1, 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, 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, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 43, 43, 43, 43, 43, 43, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183077857 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183077857 Building ZINC000183406092 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183406092 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/49 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ncccc2Br)cc1) `ZINC000183406092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183406092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183406092 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ncccc2Br)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.ar', 'N.ar', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 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] 0 hydrogens need 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, 5, 5, 12, 12, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 39, 39, 39, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/50 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ncccc2Br)cc1) `ZINC000183406092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183406092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183406092 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ncccc2Br)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.ar', 'N.ar', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 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] 0 hydrogens need 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, 6, 6, 13, 13, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183406092 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 Building ZINC000183406092 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183406092 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 49) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N(C)c2ncccc2Br)cc1) `ZINC000183406092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183406092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183406092 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2ncccc2Br)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.ar', 'N.ar', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 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] 0 hydrogens need 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, 5, 5, 12, 12, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 39, 39, 39, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 50) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N(C)c2ncccc2Br)cc1) `ZINC000183406092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183406092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183406092 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2ncccc2Br)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.ar', 'N.ar', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 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] 0 hydrogens need 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, 6, 6, 13, 13, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 38, 38, 38, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183406092 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183406092 Building ZINC000183566105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183566105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/51 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ncnc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C) `ZINC000183566105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183566105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000183566105 none Cc1[nH]c2ncnc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/52 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ncnc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C) `ZINC000183566105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183566105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000183566105 none Cc1[nH]c2ncnc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183566105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 Building ZINC000183566105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183566105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 51) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1[nH]c2ncnc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C) `ZINC000183566105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183566105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000183566105 none Cc1[nH]c2ncnc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 52) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1[nH]c2ncnc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C) `ZINC000183566105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183566105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000183566105 none Cc1[nH]c2ncnc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183566105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183566105 Building ZINC000183733873 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733873 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/53 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C) `ZINC000183733873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733873 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30] 48 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 75 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/54 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C) `ZINC000183733873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733873 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733873 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 Building ZINC000183733873 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733873 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 53) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C) `ZINC000183733873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733873 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30] 48 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 75 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 54) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C) `ZINC000183733873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733873 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733873 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733873 Building ZINC000183733892 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733892 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/55 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C) `ZINC000183733892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733892 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/56 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C) `ZINC000183733892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733892 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733892 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 Building ZINC000183733892 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733892 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 55) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C) `ZINC000183733892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733892 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 56) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C) `ZINC000183733892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733892 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1c(C)nn(C)c1C 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', 'H', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733892 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733892 Building ZINC000183733964 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733964 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/57 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nccn1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733964 none CCc1nccn1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 8, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 13, 46, 46, 46, 46, 46, 32, 32, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 13, 13] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/58 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nccn1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733964 none CCc1nccn1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 6, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 11, 47, 47, 47, 47, 47, 32, 32, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733964 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 Building ZINC000183733964 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733964 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 57) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCc1nccn1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733964 none CCc1nccn1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 8, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 13, 46, 46, 46, 46, 46, 32, 32, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 13, 13] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 58) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCc1nccn1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733964 none CCc1nccn1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 6, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 11, 47, 47, 47, 47, 47, 32, 32, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733964 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733964 Building ZINC000183733978 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733978 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/59 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nccn1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733978 none CCc1nccn1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 8, 1, 7, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 12, 46, 46, 46, 46, 46, 31, 31, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/60 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nccn1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733978 none CCc1nccn1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 7, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 12, 48, 48, 48, 48, 48, 30, 30, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 12, 12] 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]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733978 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 Building ZINC000183733978 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733978 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 59) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nccn1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733978 none CCc1nccn1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 8, 1, 7, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 12, 46, 46, 46, 46, 46, 31, 31, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 60) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nccn1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1) `ZINC000183733978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000183733978 none CCc1nccn1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 7, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 12, 48, 48, 48, 48, 48, 30, 30, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 12, 12] 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]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183733978 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183733978 Building ZINC000183760022 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183760022 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/61 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)cc1) `ZINC000183760022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183760022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183760022 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 43, 43, 43, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/62 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)cc1) `ZINC000183760022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183760022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183760022 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 17, 44, 44, 25, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 44, 44, 44, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183760022 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 Building ZINC000183760022 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183760022 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 61) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)cc1) `ZINC000183760022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183760022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183760022 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 43, 43, 43, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 62) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)cc1) `ZINC000183760022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183760022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183760022 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc([N+](=O)[O-])cc2Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 17, 44, 44, 25, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 44, 44, 44, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183760022 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183760022 Building ZINC000183913745 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183913745 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/63 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)c2)cc1) `ZINC000183913745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183913745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183913745 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 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, 7] 0 hydrogens need 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, 4, 4, 10, 26, 26, 26, 26, 26, 44, 46, 46, 46, 46, 43, 5, 5, 5, 5, 5, 5, 5, 10, 26, 26, 46, 46, 46, 46, 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]) total number of confs: 118 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/64 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)c2)cc1) `ZINC000183913745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183913745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183913745 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 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, 7] 0 hydrogens need 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, 10, 27, 27, 27, 27, 27, 46, 46, 46, 46, 46, 43, 6, 6, 6, 6, 6, 6, 6, 10, 27, 27, 46, 46, 46, 46, 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]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183913745 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 Building ZINC000183913745 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183913745 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 63) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)c2)cc1) `ZINC000183913745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183913745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183913745 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 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, 7] 0 hydrogens need 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, 4, 4, 10, 26, 26, 26, 26, 26, 44, 46, 46, 46, 46, 43, 5, 5, 5, 5, 5, 5, 5, 10, 26, 26, 46, 46, 46, 46, 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]) total number of confs: 118 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 64) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)c2)cc1) `ZINC000183913745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183913745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000183913745 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2c2cccc(F)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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 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, 7] 0 hydrogens need 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, 10, 27, 27, 27, 27, 27, 46, 46, 46, 46, 46, 43, 6, 6, 6, 6, 6, 6, 6, 10, 27, 27, 46, 46, 46, 46, 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]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183913745 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183913745 Building ZINC000183919932 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183919932 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/65 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183919932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183919932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183919932 none CCn1cc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 28, 28, 50, 50, 50, 50, 50, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/66 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183919932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183919932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183919932 none CCn1cc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 13, 13, 13, 13, 5, 1, 9, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 13, 13, 33, 33, 50, 50, 50, 50, 50, 33, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183919932 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 Building ZINC000183919932 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183919932 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 65) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183919932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183919932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183919932 none CCn1cc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 28, 28, 50, 50, 50, 50, 50, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 66) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183919932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183919932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183919932 none CCn1cc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 13, 13, 13, 13, 5, 1, 9, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 13, 13, 33, 33, 50, 50, 50, 50, 50, 33, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183919932 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183919932 Building ZINC000183962643 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183962643 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/67 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1) `ZINC000183962643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183962643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962643 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 45, 45, 32, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/68 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1) `ZINC000183962643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183962643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962643 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183962643 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 Building ZINC000183962643 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183962643 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 67) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1) `ZINC000183962643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183962643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962643 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 45, 45, 32, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 68) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1) `ZINC000183962643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183962643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962643 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183962643 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962643 Building ZINC000183962665 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183962665 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/69 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1) `ZINC000183962665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183962665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962665 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 50, 50, 25, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/70 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1) `ZINC000183962665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183962665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962665 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 46, 46, 31, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183962665 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 Building ZINC000183962665 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183962665 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 69) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1) `ZINC000183962665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183962665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962665 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 50, 50, 25, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 70) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1) `ZINC000183962665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183962665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183962665 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1noc(C(C)C)n1 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', 'H', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 12, 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, 3, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 46, 46, 31, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183962665 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183962665 Building ZINC000184060235 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184060235 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/71 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C) `ZINC000184060235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184060235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000184060235 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 28, 28, 28, 28, 39, 39, 39, 39, 28, 28, 28, 12, 12, 12, 9, 9, 9, 9, 8, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/72 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C) `ZINC000184060235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184060235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000184060235 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 29, 29, 29, 29, 39, 39, 39, 39, 29, 29, 29, 12, 12, 12, 9, 9, 9, 9, 7, 29, 29, 39, 39, 39, 39, 39, 39, 39, 39, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184060235 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 Building ZINC000184060235 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184060235 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 71) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C) `ZINC000184060235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184060235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000184060235 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 28, 28, 28, 28, 39, 39, 39, 39, 28, 28, 28, 12, 12, 12, 9, 9, 9, 9, 8, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 72) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C) `ZINC000184060235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184060235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000184060235 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 29, 29, 29, 29, 39, 39, 39, 39, 29, 29, 29, 12, 12, 12, 9, 9, 9, 9, 7, 29, 29, 39, 39, 39, 39, 39, 39, 39, 39, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184060235 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184060235 Building ZINC000184366153 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184366153 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/73 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184366153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9] 27 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: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/74 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184366153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 1, 9, 9, 1, 1, 1, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9] 22 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: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184366153 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 Building ZINC000184366153 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184366153 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 73) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184366153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9] 27 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: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 74) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184366153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 1, 9, 9, 1, 1, 1, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9] 22 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: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184366153 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366153 Building ZINC000184366169 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184366169 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/75 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184366169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366169 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8] 21 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/76 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184366169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366169 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11] 27 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: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184366169 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 Building ZINC000184366169 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184366169 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 75) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N2C[C@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184366169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366169 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8] 21 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 76) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N2C[C@H]3CCC(=O)c4cccc2c43)cc1) `ZINC000184366169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184366169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000184366169 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H]3CCC(=O)c4cccc2c43)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.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 11, 1, 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: [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, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11] 27 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: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184366169 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184366169 Building ZINC000185212940 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185212940 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/77 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185212940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212940 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 24, 24, 24, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 24, 24, 24, 72, 48, 48, 48, 48, 4, 4] 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]) total number of confs: 231 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/78 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185212940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212940 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 24, 24, 24, 72, 48, 48, 48, 48, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 226 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185212940 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 Building ZINC000185212940 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185212940 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 77) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185212940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212940 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 24, 24, 24, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 24, 24, 24, 72, 48, 48, 48, 48, 4, 4] 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]) total number of confs: 231 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 78) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185212940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212940 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 24, 24, 24, 72, 48, 48, 48, 48, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 226 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185212940 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212940 Building ZINC000185212956 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185212956 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/79 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185212956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212956 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 48, 48, 41, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 24, 24, 24, 72, 48, 48, 48, 48, 4, 4] 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]) total number of confs: 258 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/80 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185212956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212956 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 23, 23, 23, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 23, 23, 23, 69, 48, 48, 48, 48, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185212956 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 Building ZINC000185212956 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185212956 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 79) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185212956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212956 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 48, 48, 41, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 24, 24, 24, 72, 48, 48, 48, 48, 4, 4] 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]) total number of confs: 258 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 80) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)c2)cc1) `ZINC000185212956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185212956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185212956 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)c2cccc(Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 23, 23, 23, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 23, 23, 23, 69, 48, 48, 48, 48, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 229 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185212956 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185212956 Building ZINC000185408348 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185408348 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/81 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000185408348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185408348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185408348 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 1, 2, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 41, 41, 41, 41, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/82 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000185408348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185408348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185408348 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 4, 4, 18, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 40, 40, 40, 40, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185408348 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 Building ZINC000185408348 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185408348 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 81) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000185408348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185408348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185408348 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 1, 2, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 41, 41, 41, 41, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 82) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000185408348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185408348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185408348 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 4, 4, 18, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 40, 40, 40, 40, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185408348 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185408348 Building ZINC000185571013 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185571013 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/83 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/83' -> `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)Oc3c(F)cccc32)cc1) `ZINC000185571013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185571013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571013 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 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: [8, 1, 1, 8, 8, 1, 1, 1, 3, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8] 39 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/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/84 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/84' -> `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)Oc3c(F)cccc32)cc1) `ZINC000185571013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185571013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571013 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 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: [8, 1, 1, 8, 8, 1, 1, 1, 3, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8] 39 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185571013 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 Building ZINC000185571013 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185571013 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 83) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)Oc3c(F)cccc32)cc1) `ZINC000185571013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185571013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571013 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 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: [8, 1, 1, 8, 8, 1, 1, 1, 3, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8] 39 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/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 84) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)Oc3c(F)cccc32)cc1) `ZINC000185571013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185571013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571013 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 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: [8, 1, 1, 8, 8, 1, 1, 1, 3, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8] 39 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185571013 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571013 Building ZINC000185571028 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185571028 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/85 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/85' -> `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)Oc3c(F)cccc32)cc1) `ZINC000185571028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185571028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571028 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 1, 8, 8, 1, 1, 1, 2, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8] 38 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/86 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/86' -> `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)Oc3c(F)cccc32)cc1) `ZINC000185571028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185571028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571028 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 2, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8] 35 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185571028 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 Building ZINC000185571028 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185571028 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 85) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)Oc3c(F)cccc32)cc1) `ZINC000185571028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185571028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571028 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 1, 8, 8, 1, 1, 1, 2, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8] 38 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 86) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)Oc3c(F)cccc32)cc1) `ZINC000185571028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185571028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185571028 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C)Oc3c(F)cccc32)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 8, 8, 1, 1, 1, 2, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8] 35 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185571028 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185571028 Building ZINC000185738618 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185738618 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/87 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1) `ZINC000185738618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185738618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000185738618 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 18, 19, 31, 31, 8, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 19, 19, 31, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/88 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1) `ZINC000185738618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185738618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000185738618 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 19, 20, 33, 33, 9, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 19, 19, 20, 20, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185738618 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 Building ZINC000185738618 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185738618 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 87) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1) `ZINC000185738618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185738618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000185738618 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 18, 19, 31, 31, 8, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 19, 19, 31, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 88) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1) `ZINC000185738618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185738618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000185738618 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 19, 20, 33, 33, 9, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 19, 19, 20, 20, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185738618 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185738618 Building ZINC000185809255 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185809255 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/89 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1) `ZINC000185809255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185809255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000185809255 none COCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens 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, 41, 41, 26, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 3, 3, 39, 39, 39, 39, 39, 47, 47, 47, 41, 41, 41, 41, 11, 11, 2, 3, 3, 5, 5, 5, 3, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 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: 202 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/90 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1) `ZINC000185809255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185809255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000185809255 none COCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens 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, 41, 41, 26, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 40, 40, 40, 40, 40, 47, 47, 47, 41, 41, 41, 41, 11, 11, 2, 3, 3, 5, 5, 5, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185809255 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 Building ZINC000185809255 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185809255 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 89) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1) `ZINC000185809255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185809255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000185809255 none COCCC1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens 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, 41, 41, 26, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 3, 3, 39, 39, 39, 39, 39, 47, 47, 47, 41, 41, 41, 41, 11, 11, 2, 3, 3, 5, 5, 5, 3, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 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: 202 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 90) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1) `ZINC000185809255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185809255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000185809255 none COCCC1(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens 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, 41, 41, 26, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 40, 40, 40, 40, 40, 47, 47, 47, 41, 41, 41, 41, 11, 11, 2, 3, 3, 5, 5, 5, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185809255 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185809255 Building ZINC000185929571 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185929571 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/91 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)cc1) `ZINC000185929571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185929571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929571 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 12, 46, 46, 46, 38, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/92 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)cc1) `ZINC000185929571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185929571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929571 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 5, 13, 49, 49, 49, 39, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185929571 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 Building ZINC000185929571 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185929571 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 91) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)cc1) `ZINC000185929571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185929571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929571 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 12, 46, 46, 46, 38, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 92) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)cc1) `ZINC000185929571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185929571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929571 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 5, 13, 49, 49, 49, 39, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185929571 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929571 Building ZINC000185929592 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185929592 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/93 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)OCc2ccccc23)cc1) `ZINC000185929592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185929592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929592 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 5, 9, 45, 48, 48, 42, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 48, 48, 48, 48, 48, 48, 48, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/94 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)OCc2ccccc23)cc1) `ZINC000185929592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185929592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929592 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 8, 42, 45, 45, 39, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185929592 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 Building ZINC000185929592 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185929592 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 93) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N2CC[C@@]3(C2)OCc2ccccc23)cc1) `ZINC000185929592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185929592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929592 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 5, 9, 45, 48, 48, 42, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 48, 48, 48, 48, 48, 48, 48, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 94) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N2CC[C@@]3(C2)OCc2ccccc23)cc1) `ZINC000185929592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185929592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185929592 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)OCc2ccccc23)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need 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, 8, 42, 45, 45, 39, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185929592 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185929592 Building ZINC000185910348 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185910348 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/95 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)cn2)cc1) `ZINC000185910348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185910348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185910348 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)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.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 32, 32, 14, 15, 46, 46, 27, 46, 46, 32, 32, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 32, 46, 46, 38, 46, 46, 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: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/96 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)cn2)cc1) `ZINC000185910348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185910348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185910348 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)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.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 30, 30, 12, 14, 45, 45, 25, 45, 45, 30, 30, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 30, 45, 45, 31, 45, 45, 30, 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: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185910348 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 Building ZINC000185910348 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185910348 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 95) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCc2ncc(c3ccccc3)cn2)cc1) `ZINC000185910348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185910348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185910348 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)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.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 32, 32, 14, 15, 46, 46, 27, 46, 46, 32, 32, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 32, 46, 46, 38, 46, 46, 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: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 96) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCc2ncc(c3ccccc3)cn2)cc1) `ZINC000185910348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185910348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185910348 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ncc(c3ccccc3)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.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 30, 30, 12, 14, 45, 45, 25, 45, 45, 30, 30, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 30, 45, 45, 31, 45, 45, 30, 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: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185910348 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185910348 Building ZINC000185943992 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185943992 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/97 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185943992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185943992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185943992 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 16, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 41, 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, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/98 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185943992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185943992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185943992 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 38, 38, 7, 7, 7, 7, 7, 7, 7, 5, 20, 20, 20, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185943992 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 Building ZINC000185943992 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185943992 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 97) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185943992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185943992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185943992 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 16, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 41, 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, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 98) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185943992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185943992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185943992 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 38, 38, 7, 7, 7, 7, 7, 7, 7, 5, 20, 20, 20, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 38, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185943992 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185943992 Building ZINC000185944008 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185944008 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/99 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185944008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185944008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944008 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 40, 40, 9, 9, 9, 9, 9, 9, 9, 5, 21, 21, 21, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/100 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185944008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185944008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944008 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 41, 41, 7, 7, 7, 7, 7, 7, 7, 5, 18, 18, 18, 37, 37, 37, 37, 37, 41, 41, 41, 41, 41, 41, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185944008 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 Building ZINC000185944008 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185944008 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 99) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N[C@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185944008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185944008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944008 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 40, 40, 9, 9, 9, 9, 9, 9, 9, 5, 21, 21, 21, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 100) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N[C@H](C)[C@@H](c2ccccc2)N(C)C)cc1) `ZINC000185944008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185944008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944008 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 41, 41, 7, 7, 7, 7, 7, 7, 7, 5, 18, 18, 18, 37, 37, 37, 37, 37, 41, 41, 41, 41, 41, 41, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185944008 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944008 Building ZINC000185944027 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185944027 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/101 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185944027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944027 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 40, 40, 9, 9, 9, 9, 9, 9, 9, 5, 21, 21, 21, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 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, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/102 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185944027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944027 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 38, 38, 8, 8, 8, 8, 8, 8, 8, 5, 22, 22, 22, 36, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185944027 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 Building ZINC000185944027 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185944027 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 101) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185944027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944027 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 40, 40, 9, 9, 9, 9, 9, 9, 9, 5, 21, 21, 21, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 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, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 102) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185944027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944027 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 38, 38, 8, 8, 8, 8, 8, 8, 8, 5, 22, 22, 22, 36, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185944027 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944027 Building ZINC000185944049 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185944049 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/103 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185944049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944049 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 7, 7, 7, 7, 7, 7, 7, 5, 17, 17, 17, 35, 35, 35, 35, 35, 38, 38, 38, 38, 38, 38, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/104 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185944049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944049 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 16, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 41, 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, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185944049 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 Building ZINC000185944049 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185944049 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 103) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185944049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944049 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [7, 1, 1, 7, 7, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 7, 7, 7, 7, 7, 7, 7, 5, 17, 17, 17, 35, 35, 35, 35, 35, 38, 38, 38, 38, 38, 38, 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, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 104) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)cc1) `ZINC000185944049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185944049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000185944049 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)[C@H](c2ccccc2)N(C)C)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 10, 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] 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 16, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 41, 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, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185944049 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185944049 Building ZINC000186065726 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186065726 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/105 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1) `ZINC000186065726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186065726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065726 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 22, 45, 50, 50, 45, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 13, 13, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/106 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1) `ZINC000186065726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186065726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065726 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 15, 27, 48, 50, 50, 48, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 15, 15, 48, 48, 50, 50, 48, 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]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186065726 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 Building ZINC000186065726 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186065726 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 105) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1) `ZINC000186065726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186065726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065726 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 22, 45, 50, 50, 45, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 13, 13, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 106) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1) `ZINC000186065726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186065726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065726 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 15, 27, 48, 50, 50, 48, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 15, 15, 48, 48, 50, 50, 48, 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]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186065726 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065726 Building ZINC000186065743 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186065743 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/107 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1) `ZINC000186065743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186065743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065743 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 15, 27, 49, 50, 50, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 15, 15, 49, 49, 50, 50, 49, 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]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/108 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1) `ZINC000186065743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186065743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065743 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 22, 46, 50, 50, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 13, 13, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186065743 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 Building ZINC000186065743 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186065743 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 107) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1) `ZINC000186065743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186065743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065743 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 15, 27, 49, 50, 50, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 15, 15, 49, 49, 50, 50, 49, 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]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 108) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1) `ZINC000186065743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186065743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186065743 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 22, 46, 50, 50, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 13, 13, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186065743 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186065743 Building ZINC000186055274 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186055274 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/109 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)cc1) `ZINC000186055274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186055274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055274 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 2, 10, 12, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 50, 50, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/110 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)cc1) `ZINC000186055274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186055274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055274 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 49, 49, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186055274 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 Building ZINC000186055274 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186055274 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 109) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)cc1) `ZINC000186055274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186055274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055274 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 2, 10, 12, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 50, 50, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 110) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)cc1) `ZINC000186055274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186055274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055274 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 49, 49, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186055274 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055274 Building ZINC000186055296 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186055296 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/111 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)cc1) `ZINC000186055296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186055296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055296 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 49, 49, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/112 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)cc1) `ZINC000186055296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186055296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055296 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 2, 9, 11, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 50, 50, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186055296 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 Building ZINC000186055296 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186055296 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 111) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)cc1) `ZINC000186055296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186055296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055296 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 49, 49, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 112) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)cc1) `ZINC000186055296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186055296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186055296 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCSC[C@H]2c2nccs2)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', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 5, 7, 1, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 2, 9, 11, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 50, 50, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186055296 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186055296 Building ZINC000186078496 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186078496 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/113 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186078496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078496 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 27, 27, 27, 27, 27, 50, 50, 50, 50, 27, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 27, 27, 27, 50, 50, 50, 27] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/114 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186078496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078496 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 29, 29, 29, 29, 29, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 29, 29, 29, 50, 50, 50, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186078496 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 Building ZINC000186078496 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186078496 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 113) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186078496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078496 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 27, 27, 27, 27, 27, 50, 50, 50, 50, 27, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 27, 27, 27, 50, 50, 50, 27] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 114) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186078496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078496 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 29, 29, 29, 29, 29, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 29, 29, 29, 50, 50, 50, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186078496 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078496 Building ZINC000186078512 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186078512 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/115 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186078512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078512 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 29, 29, 29, 29, 29, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 29, 29, 29, 50, 50, 50, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/116 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186078512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078512 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 26, 26, 26, 26, 26, 50, 50, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 26, 26, 26, 50, 50, 50, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186078512 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 Building ZINC000186078512 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186078512 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 115) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186078512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078512 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 29, 29, 29, 29, 29, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 29, 29, 29, 50, 50, 50, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 116) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1) `ZINC000186078512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186078512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186078512 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cccc(n2ccnc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 26, 26, 26, 26, 26, 50, 50, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 26, 26, 26, 50, 50, 50, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186078512 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186078512 Building ZINC000186081705 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186081705 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/117 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1) `ZINC000186081705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186081705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081705 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 18, 18, 31, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/118 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1) `ZINC000186081705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186081705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081705 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 24, 24, 36, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 4, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186081705 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 Building ZINC000186081705 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186081705 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 117) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1) `ZINC000186081705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186081705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081705 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 18, 18, 31, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 118) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1) `ZINC000186081705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186081705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081705 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 24, 24, 36, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 4, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186081705 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081705 Building ZINC000186081724 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186081724 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/119 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1) `ZINC000186081724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186081724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081724 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 24, 24, 37, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 4, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/120 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1) `ZINC000186081724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186081724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081724 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 16, 16, 31, 50, 50, 50, 50, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186081724 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 Building ZINC000186081724 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186081724 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 119) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1) `ZINC000186081724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186081724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081724 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 24, 24, 37, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 4, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 120) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1) `ZINC000186081724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186081724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186081724 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(C2CCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 16, 16, 31, 50, 50, 50, 50, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186081724 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186081724 Building ZINC000186097911 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186097911 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/121 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186097911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097911 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 5, 6, 6, 1, 1, 1, 1, 7, 7, 12, 31, 31, 31, 31, 31, 31, 31, 41, 41, 31, 41, 41, 7, 7, 7, 6, 6, 6, 6, 7, 31, 31, 31, 31, 41, 41, 31, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/122 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186097911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097911 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 43, 43, 34, 43, 43, 5, 5, 5, 5, 5, 5, 5, 6, 34, 34, 34, 34, 43, 43, 38, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186097911 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 Building ZINC000186097911 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186097911 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 121) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186097911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097911 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 5, 6, 6, 1, 1, 1, 1, 7, 7, 12, 31, 31, 31, 31, 31, 31, 31, 41, 41, 31, 41, 41, 7, 7, 7, 6, 6, 6, 6, 7, 31, 31, 31, 31, 41, 41, 31, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 122) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186097911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097911 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 43, 43, 34, 43, 43, 5, 5, 5, 5, 5, 5, 5, 6, 34, 34, 34, 34, 43, 43, 38, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186097911 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097911 Building ZINC000186097927 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186097927 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/123 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186097927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097927 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 40, 40, 37, 40, 40, 6, 6, 6, 5, 5, 5, 5, 6, 34, 34, 34, 34, 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]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/124 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186097927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097927 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 6, 6, 12, 34, 34, 34, 34, 34, 34, 34, 42, 42, 34, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 42, 42, 34, 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]) total number of confs: 149 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186097927 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 Building ZINC000186097927 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186097927 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 123) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186097927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097927 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 40, 40, 37, 40, 40, 6, 6, 6, 5, 5, 5, 5, 6, 34, 34, 34, 34, 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]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 124) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1) `ZINC000186097927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186097927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097927 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 6, 6, 12, 34, 34, 34, 34, 34, 34, 34, 42, 42, 34, 42, 42, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 42, 42, 34, 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]) total number of confs: 149 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186097927 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097927 Building ZINC000186097968 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186097968 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/125 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1) `ZINC000186097968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186097968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097968 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 5, 5, 1, 1, 1, 1, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 43, 43, 39, 43, 43, 5, 5, 5, 5, 5, 5, 5, 6, 34, 34, 34, 34, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/126 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1) `ZINC000186097968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186097968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097968 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 7, 7, 12, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 39, 39, 7, 7, 7, 6, 6, 6, 6, 7, 32, 32, 32, 32, 39, 39, 32, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186097968 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 Building ZINC000186097968 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186097968 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 125) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1) `ZINC000186097968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186097968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097968 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 5, 5, 1, 1, 1, 1, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 43, 43, 39, 43, 43, 5, 5, 5, 5, 5, 5, 5, 6, 34, 34, 34, 34, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 126) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1) `ZINC000186097968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186097968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186097968 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 7, 7, 12, 32, 32, 32, 32, 32, 32, 32, 39, 39, 32, 39, 39, 7, 7, 7, 6, 6, 6, 6, 7, 32, 32, 32, 32, 39, 39, 32, 39, 39] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186097968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186097968 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186097968 Building ZINC000118262923 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000118262923 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/127 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118262923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000118262923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118262923 none CC(=O)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 11, 19, 11, 11, 6, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 19, 11, 11, 11, 11, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/128 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118262923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000118262923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118262923 none CC(=O)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 20, 11, 11, 6, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 20, 20, 20, 11, 11, 11, 11, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000118262923 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 Building ZINC000118262923 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000118262923 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 127) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(=O)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118262923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000118262923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118262923 none CC(=O)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 11, 19, 11, 11, 6, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 19, 11, 11, 11, 11, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 128) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(=O)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118262923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000118262923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118262923 none CC(=O)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 20, 11, 11, 6, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 20, 20, 20, 11, 11, 11, 11, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000118262923 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118262923 Building ZINC000186121330 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186121330 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/129 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121330 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 15, 6, 15, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 15, 30, 30, 22, 30, 30, 41, 41, 41, 38, 38, 15, 15, 15, 6, 3, 3, 3, 3, 3, 3, 3, 30, 30, 28, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/130 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121330 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 14, 6, 14, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 14, 25, 25, 17, 25, 25, 39, 39, 39, 36, 36, 14, 14, 14, 6, 3, 3, 3, 3, 3, 3, 3, 25, 25, 23, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186121330 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 Building ZINC000186121330 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186121330 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 129) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121330 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 15, 6, 15, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 15, 30, 30, 22, 30, 30, 41, 41, 41, 38, 38, 15, 15, 15, 6, 3, 3, 3, 3, 3, 3, 3, 30, 30, 28, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 130) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186121330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121330 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 14, 6, 14, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 14, 25, 25, 17, 25, 25, 39, 39, 39, 36, 36, 14, 14, 14, 6, 3, 3, 3, 3, 3, 3, 3, 25, 25, 23, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186121330 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121330 Building ZINC000186121346 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186121346 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/131 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186121346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121346 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 14, 6, 14, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 14, 25, 25, 14, 25, 25, 40, 40, 40, 37, 37, 14, 14, 14, 6, 3, 3, 3, 3, 3, 3, 3, 25, 25, 14, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/132 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186121346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121346 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 15, 6, 15, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 15, 29, 29, 15, 29, 29, 41, 41, 41, 38, 38, 15, 15, 15, 6, 3, 3, 3, 3, 3, 3, 3, 29, 29, 15, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186121346 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 Building ZINC000186121346 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186121346 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 131) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186121346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121346 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 14, 6, 14, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 14, 25, 25, 14, 25, 25, 40, 40, 40, 37, 37, 14, 14, 14, 6, 3, 3, 3, 3, 3, 3, 3, 25, 25, 14, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 132) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1) `ZINC000186121346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186121346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186121346 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccccc1OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 15, 6, 15, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 15, 29, 29, 15, 29, 29, 41, 41, 41, 38, 38, 15, 15, 15, 6, 3, 3, 3, 3, 3, 3, 3, 29, 29, 15, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186121346 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186121346 Building ZINC000186125735 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186125735 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/133 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/134 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/135 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/135' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/136 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/136' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186125735 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 Building ZINC000186125735 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186125735 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 133) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 134) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 135) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 136) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186125735 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 Building ZINC000186125735 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186125735 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 133) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 134) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 135) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 136) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186125735 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 Building ZINC000186125735 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186125735 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 133) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 134) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 1, 8, 8, 1, 1, 1, 2, 12, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 45 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 135) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 136) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C) `ZINC000186125735.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186125735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186125735 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2N(C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000186125735 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186125735 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186125735 Building ZINC000186158422 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186158422 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/137 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)nn2C)cc1) `ZINC000186158422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186158422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186158422 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 5, 1, 5, 15, 15, 15, 8, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 11, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/138 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)nn2C)cc1) `ZINC000186158422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186158422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186158422 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 5, 1, 5, 15, 15, 15, 8, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 9, 11, 33, 33, 33, 33, 33, 33, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186158422 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 Building ZINC000186158422 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186158422 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 137) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)Nc2c(C)c(C(F)(F)F)nn2C)cc1) `ZINC000186158422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186158422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186158422 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 5, 1, 5, 15, 15, 15, 8, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 1, 1, 1, 1, 5, 5, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 8, 11, 32, 32, 32, 32, 32, 32, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 138) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)Nc2c(C)c(C(F)(F)F)nn2C)cc1) `ZINC000186158422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186158422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186158422 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)nn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 5, 1, 5, 15, 15, 15, 8, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 9, 11, 33, 33, 33, 33, 33, 33, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186158422 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186158422 Building ZINC000186185102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186185102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/139 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1) `ZINC000186185102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186185102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186185102 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 27, 37, 37, 37, 27, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 11, 6, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/140 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1) `ZINC000186185102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186185102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186185102 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 27, 37, 37, 37, 27, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 11, 6, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186185102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 Building ZINC000186185102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186185102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 139) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1) `ZINC000186185102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186185102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186185102 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 27, 37, 37, 37, 27, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 11, 6, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 140) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1) `ZINC000186185102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186185102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186185102 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(cc2F)NC(=O)CC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 27, 37, 37, 37, 27, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 11, 11, 11, 6, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186185102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185102 Building ZINC000186273217 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186273217 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/141 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br) `ZINC000186273217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186273217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186273217 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 15, 15, 36, 36, 36, 36, 36, 36, 7, 7, 7, 6, 6, 6, 6, 15, 15, 15, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/142 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br) `ZINC000186273217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186273217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186273217 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 15, 15, 36, 36, 36, 36, 36, 36, 7, 7, 7, 6, 6, 6, 6, 15, 15, 15, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186273217 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 Building ZINC000186273217 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186273217 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 141) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br) `ZINC000186273217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186273217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186273217 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 15, 15, 36, 36, 36, 36, 36, 36, 7, 7, 7, 6, 6, 6, 6, 15, 15, 15, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 142) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br) `ZINC000186273217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186273217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000186273217 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ncccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 17, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 15, 15, 36, 36, 36, 36, 36, 36, 7, 7, 7, 6, 6, 6, 6, 15, 15, 15, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186273217 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186273217 Building ZINC000186651306 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186651306 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/143 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cc1) `ZINC000186651306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186651306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186651306 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)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.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 1 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 11, 6, 35, 35, 105, 35, 11, 11] 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/144 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cc1) `ZINC000186651306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186651306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186651306 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)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.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 1 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11, 11, 11, 11, 6, 34, 34, 102, 34, 11, 11] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186651306 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 Building ZINC000186651306 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186651306 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 143) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cc1) `ZINC000186651306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186651306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186651306 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)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.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 1 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 11, 6, 35, 35, 105, 35, 11, 11] 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 144) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)cc1) `ZINC000186651306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186651306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186651306 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(S)[nH]c3c2)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.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 14, 8, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 1 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11, 11, 11, 11, 6, 34, 34, 102, 34, 11, 11] 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186651306 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186651306 Building ZINC000186785078 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186785078 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/145 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/146 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/147 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/147' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/148 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/148' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186785078 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 Building ZINC000186785078 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186785078 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 145) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 146) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 147) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 148) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186785078 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 Building ZINC000186785078 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186785078 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 145) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 146) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 147) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 148) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186785078 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 Building ZINC000186785078 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186785078 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 145) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 146) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 147) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 13, 18, 24, 24, 24, 24, 46, 46, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 46, 46, 46, 46, 46, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 148) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)cc1) `ZINC000186785078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186785078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186785078 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3CC3)c3ccccc32)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.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 3, 14, 19, 24, 24, 24, 24, 43, 43, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 43, 43, 43, 43, 43, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186785078 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186785078 Building ZINC000794161009 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000794161009 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/149 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000794161009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000794161009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000794161009 none COc1ccc([C@@H]2C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 24, 24, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 24, 24, 24, 24, 24, 24, 24, 11, 11, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/150 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000794161009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000794161009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000794161009 none COc1ccc([C@@H]2C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 11, 21, 21, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 21, 21, 21, 21, 21, 21, 21, 11, 11, 3, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000794161009 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 Building ZINC000794161009 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000794161009 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 149) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H]2C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000794161009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000794161009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000794161009 none COc1ccc([C@@H]2C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 24, 24, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 24, 24, 24, 24, 24, 24, 24, 11, 11, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 150) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H]2C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000794161009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000794161009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000794161009 none COc1ccc([C@@H]2C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 11, 21, 21, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 7, 21, 21, 21, 21, 21, 21, 21, 11, 11, 3, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000794161009 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000794161009 Building ZINC000187099336 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187099336 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/151 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)CCCC3)cc1) `ZINC000187099336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187099336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187099336 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 32, 37, 37, 37, 32, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 10, 10, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/152 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)CCCC3)cc1) `ZINC000187099336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187099336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187099336 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 32, 39, 39, 39, 32, 39, 39, 39, 39, 39, 39, 10, 10, 10, 10, 10, 10, 10, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187099336 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 Building ZINC000187099336 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187099336 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 151) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)CCCC3)cc1) `ZINC000187099336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187099336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187099336 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 32, 37, 37, 37, 32, 37, 37, 37, 37, 37, 37, 10, 10, 10, 10, 10, 10, 10, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 152) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)CCCC3)cc1) `ZINC000187099336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187099336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187099336 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cc2C#N)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 32, 39, 39, 39, 32, 39, 39, 39, 39, 39, 39, 10, 10, 10, 10, 10, 10, 10, 5, 39, 39, 39, 39, 39, 39, 39, 39, 39, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187099336 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187099336 Building ZINC000187178834 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178834 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/153 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178834 none O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 30, 17, 17, 17, 48, 48, 48, 48, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 30, 30, 90, 48, 48, 48, 17, 17, 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]) total number of confs: 230 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/154 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178834 none O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 26, 14, 14, 14, 44, 44, 44, 44, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 26, 26, 78, 44, 44, 44, 14, 14, 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]) total number of confs: 213 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178834 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 Building ZINC000187178834 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178834 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 153) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178834 none O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 30, 17, 17, 17, 48, 48, 48, 48, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 30, 30, 90, 48, 48, 48, 17, 17, 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]) total number of confs: 230 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 154) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178834 none O=C(N1C[C@H](CO)[C@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 26, 14, 14, 14, 44, 44, 44, 44, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 26, 26, 78, 44, 44, 44, 14, 14, 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]) total number of confs: 213 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178834 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178834 Building ZINC000187178856 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178856 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/155 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178856 none O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 14, 1, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 46, 46, 46, 46, 17, 17, 17, 28, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 17, 17, 46, 46, 46, 28, 28, 84, 17, 17, 2, 2, 2, 2] 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]) total number of confs: 207 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/156 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178856 none O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 14, 1, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 46, 46, 46, 46, 14, 14, 14, 26, 14, 1, 1, 1, 2, 2, 1, 2, 2, 2, 14, 14, 46, 46, 46, 26, 26, 78, 14, 14, 2, 2, 2, 2] 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]) total number of confs: 205 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178856 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 Building ZINC000187178856 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178856 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 155) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178856 none O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 14, 1, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 46, 46, 46, 46, 17, 17, 17, 28, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 17, 17, 46, 46, 46, 28, 28, 84, 17, 17, 2, 2, 2, 2] 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]) total number of confs: 207 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 156) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178856 none O=C(N1C[C@@H](c2ccsc2)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 14, 1, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 46, 46, 46, 46, 14, 14, 14, 26, 14, 1, 1, 1, 2, 2, 1, 2, 2, 2, 14, 14, 46, 46, 46, 26, 26, 78, 14, 14, 2, 2, 2, 2] 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]) total number of confs: 205 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178856 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178856 Building ZINC000187178880 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178880 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/157 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178880 none O=C(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 26, 14, 14, 14, 46, 46, 46, 46, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 26, 26, 78, 46, 46, 46, 14, 14, 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]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/158 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178880 none O=C(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 23, 14, 14, 14, 44, 44, 44, 44, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 23, 23, 69, 44, 44, 44, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178880 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 Building ZINC000187178880 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178880 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 157) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178880 none O=C(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 26, 14, 14, 14, 46, 46, 46, 46, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 26, 26, 78, 46, 46, 46, 14, 14, 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]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 158) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178880 none O=C(N1C[C@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 14, 14, 14, 14, 23, 14, 14, 14, 44, 44, 44, 44, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 23, 23, 69, 44, 44, 44, 14, 14, 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]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178880 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178880 Building ZINC000187178901 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178901 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/159 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178901 none O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 5, 15, 15, 15, 15, 27, 15, 15, 15, 44, 44, 44, 44, 15, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 27, 27, 81, 44, 44, 44, 15, 15, 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]) total number of confs: 212 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/160 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178901 none O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 30, 17, 17, 17, 48, 48, 48, 48, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 30, 30, 90, 48, 48, 48, 17, 17, 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]) total number of confs: 231 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178901 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 Building ZINC000187178901 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187178901 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 159) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187178901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178901 none O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 5, 15, 15, 15, 15, 27, 15, 15, 15, 44, 44, 44, 44, 15, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 27, 27, 81, 44, 44, 44, 15, 15, 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]) total number of confs: 212 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 160) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000187178901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187178901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000187178901 none O=C(N1C[C@@H](CO)[C@@H](c2ccsc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 30, 17, 17, 17, 48, 48, 48, 48, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 30, 30, 90, 48, 48, 48, 17, 17, 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]) total number of confs: 231 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187178901 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187178901 Building ZINC000187249247 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187249247 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/161 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)n2)cc1) `ZINC000187249247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187249247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187249247 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 17, 8, 1, 1, 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] 0 hydrogens need 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, 10, 10, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 40, 40, 40, 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]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/162 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)n2)cc1) `ZINC000187249247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187249247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187249247 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 17, 8, 1, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 10, 10, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 41, 41, 41, 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187249247 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 Building ZINC000187249247 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187249247 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 161) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)n2)cc1) `ZINC000187249247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187249247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187249247 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 17, 8, 1, 1, 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] 0 hydrogens need 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, 10, 10, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 40, 40, 40, 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]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 162) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)n2)cc1) `ZINC000187249247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187249247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000187249247 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 17, 8, 1, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 10, 10, 41, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 41, 41, 41, 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187249247 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187249247 Building ZINC000278560063 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278560063 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/163 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C) `ZINC000278560063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278560063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560063 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 12, 33, 33, 33, 33, 33, 33, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 4, 6, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/164 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C) `ZINC000278560063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278560063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560063 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need 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, 17, 17, 7, 17, 17, 4, 4, 1, 1, 1, 1, 8, 8, 13, 32, 32, 32, 32, 32, 32, 4, 4, 4, 17, 17, 7, 17, 17, 4, 4, 4, 8, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 122 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000278560063 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 Building ZINC000278560063 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278560063 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 163) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C) `ZINC000278560063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278560063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560063 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 12, 33, 33, 33, 33, 33, 33, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 4, 6, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 164) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C) `ZINC000278560063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278560063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560063 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need 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, 17, 17, 7, 17, 17, 4, 4, 1, 1, 1, 1, 8, 8, 13, 32, 32, 32, 32, 32, 32, 4, 4, 4, 17, 17, 7, 17, 17, 4, 4, 4, 8, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 122 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000278560063 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560063 Building ZINC000278560067 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278560067 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/165 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C) `ZINC000278560067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278560067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560067 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 8, 8, 14, 35, 35, 35, 35, 35, 35, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 4, 8, 35, 35, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 135 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/166 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C) `ZINC000278560067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278560067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560067 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 11, 33, 33, 33, 33, 33, 33, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 125 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000278560067 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 Building ZINC000278560067 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278560067 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 165) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C) `ZINC000278560067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278560067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560067 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 8, 8, 14, 35, 35, 35, 35, 35, 35, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 4, 8, 35, 35, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 135 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 166) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C) `ZINC000278560067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278560067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000278560067 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CSC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 11, 33, 33, 33, 33, 33, 33, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 125 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000278560067 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000278560067 Building ZINC000189007125 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189007125 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/167 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)cc1) `ZINC000189007125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189007125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189007125 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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] 0 hydrogens 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, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 6, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/168 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)cc1) `ZINC000189007125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189007125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189007125 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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] 0 hydrogens 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, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 6, 25, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189007125 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 Building ZINC000189007125 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189007125 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 167) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)cc1) `ZINC000189007125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189007125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189007125 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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] 0 hydrogens 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, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 6, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 168) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)cc1) `ZINC000189007125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189007125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189007125 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCOc3c(F)cccc32)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.ar', 'C.ar', 'F', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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] 0 hydrogens 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, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 6, 25, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189007125 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189007125 Building ZINC000189045136 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189045136 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/169 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000189045136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189045136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000189045136 none CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 27, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/170 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000189045136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189045136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000189045136 none CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 27, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189045136 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 Building ZINC000189045136 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189045136 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 169) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000189045136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189045136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000189045136 none CCSc1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 27, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 170) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1) `ZINC000189045136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189045136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000189045136 none CCSc1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 27, 27, 27, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 27, 27, 27, 50, 50, 50, 50, 50, 27, 8, 8, 2, 2, 2, 3, 3, 3, 2, 2, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189045136 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189045136 Building ZINC000189234670 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189234670 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/171 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1) `ZINC000189234670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189234670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189234670 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need 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, 4, 20, 20, 20, 20, 20, 20, 20, 43, 43, 20, 20, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 43, 43, 43, 43, 43, 43, 43, 20, 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/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/172 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1) `ZINC000189234670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189234670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189234670 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 44, 44, 20, 20, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 44, 44, 44, 44, 44, 44, 44, 20, 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189234670 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 Building ZINC000189234670 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189234670 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 171) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1) `ZINC000189234670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189234670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189234670 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need 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, 4, 20, 20, 20, 20, 20, 20, 20, 43, 43, 20, 20, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 43, 43, 43, 43, 43, 43, 43, 20, 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/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 172) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1) `ZINC000189234670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189234670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189234670 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nnc(C(C)C)n3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 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] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 44, 44, 20, 20, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 44, 44, 44, 44, 44, 44, 44, 20, 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189234670 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189234670 Building ZINC000189539980 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189539980 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/173 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)cc1) `ZINC000189539980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189539980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000189539980 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)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', 'C.2', 'Br', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 12, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/174 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)cc1) `ZINC000189539980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189539980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000189539980 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)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', 'C.2', 'Br', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 12, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189539980 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 Building ZINC000189539980 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189539980 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 173) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)cc1) `ZINC000189539980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189539980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000189539980 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)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', 'C.2', 'Br', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 12, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 174) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)cc1) `ZINC000189539980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189539980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000189539980 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(Br)o2)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', 'C.2', 'Br', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 12, 1, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000189539980 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000189539980 Building ZINC000043507106 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043507106 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/175 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1) `ZINC000043507106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043507106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000043507106 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/176 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1) `ZINC000043507106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043507106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000043507106 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000043507106 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 Building ZINC000043507106 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043507106 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 175) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1) `ZINC000043507106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043507106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000043507106 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 176) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1) `ZINC000043507106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043507106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000043507106 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cn3cc(Cl)ccc3n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000043507106 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000043507106 Building ZINC000178034830 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178034830 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/177 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178034830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000178034830 none CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 13, 24, 13, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 28, 28, 28, 28, 28, 13, 13, 13, 13, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/178 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178034830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000178034830 none CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 23, 14, 14, 14, 14, 14, 3, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000178034830 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 Building ZINC000178034830 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178034830 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 177) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178034830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000178034830 none CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 13, 24, 13, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 28, 28, 28, 28, 28, 13, 13, 13, 13, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 178) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000178034830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178034830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000178034830 none CC[S@](=O)[C@H]1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o', 'O.2', 'C.3', 'H', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 5, 7, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 23, 14, 14, 14, 14, 14, 3, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000178034830 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000178034830 Building ZINC000118993045 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000118993045 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/179 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(C2CCCC2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118993045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000118993045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118993045 none O=C(NCc1ccn(C2CCCC2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 15, 15, 15, 20, 29, 29, 29, 29, 15, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 1, 7, 7, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/180 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(C2CCCC2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118993045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000118993045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118993045 none O=C(NCc1ccn(C2CCCC2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 15, 15, 15, 20, 28, 28, 28, 28, 15, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000118993045 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 Building ZINC000118993045 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000118993045 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 179) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(C2CCCC2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118993045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000118993045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118993045 none O=C(NCc1ccn(C2CCCC2)n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 15, 15, 15, 20, 29, 29, 29, 29, 15, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 1, 7, 7, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 180) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(C2CCCC2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000118993045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000118993045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000118993045 none O=C(NCc1ccn(C2CCCC2)n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 15, 15, 15, 20, 28, 28, 28, 28, 15, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000118993045 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000118993045 Building ZINC000180594391 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180594391 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/181 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl) `ZINC000180594391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180594391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000180594391 none CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', '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, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 14, 28, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 28, 28, 28, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/182 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl) `ZINC000180594391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180594391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000180594391 none CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', '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, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 31, 31, 31, 16, 16, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180594391 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 Building ZINC000180594391 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180594391 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 181) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl) `ZINC000180594391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180594391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000180594391 none CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', '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, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 14, 28, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 28, 28, 28, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 182) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl) `ZINC000180594391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180594391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000180594391 none CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', '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, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 31, 31, 31, 16, 16, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180594391 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180594391 Building ZINC000066810126 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000066810126 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/183 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1) `ZINC000066810126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000066810126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000066810126 none Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 18, 18, 18, 18, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 18, 31, 31, 31, 31, 31, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/184 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1) `ZINC000066810126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000066810126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000066810126 none Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 29, 29, 29, 29, 29, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 50 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000066810126 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 Building ZINC000066810126 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000066810126 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 183) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1) `ZINC000066810126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000066810126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000066810126 none Cc1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 18, 18, 18, 18, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 18, 31, 31, 31, 31, 31, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 184) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1) `ZINC000066810126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000066810126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000066810126 none Cc1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 29, 29, 29, 29, 29, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 50 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000066810126 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000066810126 Building ZINC000279105712 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279105712 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/185 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21) `ZINC000279105712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279105712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000279105712 none CC(C)[C@@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 31, 40, 31, 31, 31, 22, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 40, 40, 40, 40, 40, 40, 40, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/186 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21) `ZINC000279105712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279105712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000279105712 none CC(C)[C@@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 27, 38, 27, 27, 27, 20, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 38, 38, 38, 38, 38, 38, 38, 27, 27, 11, 11, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000279105712 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 Building ZINC000279105712 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279105712 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 185) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)[C@@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21) `ZINC000279105712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279105712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000279105712 none CC(C)[C@@H]1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 31, 40, 31, 31, 31, 22, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 40, 40, 40, 40, 40, 40, 40, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 186) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)[C@@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21) `ZINC000279105712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279105712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000279105712 none CC(C)[C@@H]1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 27, 38, 27, 27, 27, 20, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 38, 38, 38, 38, 38, 38, 38, 27, 27, 11, 11, 2, 5, 5, 5, 5, 5, 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]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000279105712 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000279105712 Building ZINC000563186873 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186873 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/187 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186873 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 10, 39, 39, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/188 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186873 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 12, 12, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186873 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 Building ZINC000563186873 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186873 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 187) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186873 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 10, 39, 39, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 188) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186873 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 12, 12, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186873 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186873 Building ZINC000563186874 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186874 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/189 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186874 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 4, 4, 14, 14, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 2, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 44 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/190 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186874 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 10, 39, 39, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186874 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 Building ZINC000563186874 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186874 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 189) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186874 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 4, 4, 14, 14, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 2, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 44 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 190) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186874 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 10, 39, 39, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186874 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186874 Building ZINC000563186875 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186875 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/191 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186875 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 6, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/192 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186875 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 6, 6, 6, 6, 26, 26, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 3, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186875 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 Building ZINC000563186875 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186875 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 191) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186875 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 2, 6, 1, 1, 1, 3, 3, 1, 3, 3, 10, 10, 10, 10, 41, 41, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 192) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C) `ZINC000563186875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186875 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 6, 6, 6, 6, 26, 26, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 3, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186875 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186875 Building ZINC000563186876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/193 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186876 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 2, 2, 1, 2, 2, 10, 10, 10, 10, 42, 42, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/194 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186876 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 8, 1, 8, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 11, 44, 44, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 3, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 Building ZINC000563186876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563186876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 193) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563186876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186876 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 2, 2, 1, 2, 2, 10, 10, 10, 10, 42, 42, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 194) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C) `ZINC000563186876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563186876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000563186876 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 8, 1, 8, 1, 1, 1, 3, 3, 1, 3, 3, 11, 11, 11, 11, 44, 44, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 3, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/25650/xaq-8058115.17/working/building/ZINC000563186876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000563186876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000563186876 Building ZINC000180250951 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180250951 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/195 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000180250951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180250951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000180250951 none COc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/196 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000180250951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180250951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000180250951 none COc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180250951 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 Building ZINC000180250951 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180250951 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 195) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000180250951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180250951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000180250951 none COc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 196) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000180250951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180250951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000180250951 none COc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180250951 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180250951 Building ZINC000180280754 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180280754 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/197 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1) `ZINC000180280754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180280754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000180280754 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 17, 18, 18, 18, 7, 7, 17, 17, 17, 17, 17, 7, 4, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/198 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1) `ZINC000180280754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180280754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000180280754 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 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, 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 18, 18, 22, 24, 24, 24, 6, 6, 16, 16, 16, 16, 16, 6, 4, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 45]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180280754 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 Building ZINC000180280754 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180280754 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 197) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1) `ZINC000180280754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180280754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000180280754 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 17, 18, 18, 18, 7, 7, 17, 17, 17, 17, 17, 7, 4, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 198) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1) `ZINC000180280754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180280754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000180280754 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 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, 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] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 18, 18, 22, 24, 24, 24, 6, 6, 16, 16, 16, 16, 16, 6, 4, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 45]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180280754 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180280754 Building ZINC000337549628 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337549628 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/199 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1) `ZINC000337549628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337549628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337549628 none COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', '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, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 5, 11, 11, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 11, 11, 14, 11, 16, 16, 16, 11, 11, 3, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/200 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1) `ZINC000337549628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337549628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337549628 none COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', '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, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 5, 11, 11, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 11, 11, 14, 11, 16, 16, 16, 11, 11, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14, 14, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337549628 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 Building ZINC000337549628 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337549628 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 199) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1) `ZINC000337549628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337549628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337549628 none COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', '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, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 5, 11, 11, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 11, 11, 14, 11, 16, 16, 16, 11, 11, 3, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 200) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1) `ZINC000337549628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337549628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337549628 none COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', '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, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 5, 11, 11, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 11, 11, 14, 11, 16, 16, 16, 11, 11, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14, 14, 14, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/25650/xaq-8058115.17/working/building/ZINC000337549628 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337549628 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337549628 Building ZINC000337561624 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337561624 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/201 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000337561624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337561624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337561624 none Cc1ccc(OCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 42, 19, 12, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 44, 44, 44, 44, 44, 44, 44, 18, 18, 16, 16, 12, 12, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/202 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000337561624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337561624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337561624 none Cc1ccc(OCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 42, 18, 12, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 44, 44, 44, 44, 44, 44, 44, 17, 17, 15, 15, 11, 11, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337561624 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 Building ZINC000337561624 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337561624 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 201) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(OCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000337561624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337561624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337561624 none Cc1ccc(OCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 42, 19, 12, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 44, 44, 44, 44, 44, 44, 44, 18, 18, 16, 16, 12, 12, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 202) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(OCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000337561624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337561624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337561624 none Cc1ccc(OCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 44, 42, 18, 12, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 44, 44, 44, 44, 44, 44, 44, 17, 17, 15, 15, 11, 11, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337561624 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337561624 Building ZINC000337582612 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337582612 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/203 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337582612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582612 none CCc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 48, 48, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 3, 3, 3, 3, 13, 13, 13, 13, 13, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/204 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337582612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582612 none CCc1ccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 14, 14, 50, 50, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 3, 3, 3, 3, 14, 14, 14, 14, 14, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337582612 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 Building ZINC000337582612 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337582612 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 203) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337582612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582612 none CCc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 48, 48, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 3, 3, 3, 3, 13, 13, 13, 13, 13, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 204) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCc1ccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337582612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582612 none CCc1ccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 14, 14, 50, 50, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 3, 3, 3, 3, 14, 14, 14, 14, 14, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337582612 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582612 Building ZINC000337582613 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337582613 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/205 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337582613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582613 none CCc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 50, 50, 13, 13, 13, 13, 6, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 13, 13, 13, 13, 13, 50, 50] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/206 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337582613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582613 none CCc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 13, 13, 13, 13, 6, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 13, 13, 13, 13, 13, 50, 50] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337582613 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 Building ZINC000337582613 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337582613 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 205) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337582613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582613 none CCc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 50, 50, 13, 13, 13, 13, 6, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 13, 13, 13, 13, 13, 50, 50] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 206) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1) `ZINC000337582613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337582613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000337582613 none CCc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCN2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 1, 1, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 13, 13, 13, 13, 6, 2, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 13, 13, 13, 13, 13, 50, 50] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337582613 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337582613 Building ZINC000337648445 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337648445 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/207 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2ncccc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337648445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337648445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000337648445 none O=C(NCCc1c[nH]c2ncccc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 17, 17, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/208 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2ncccc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337648445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337648445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000337648445 none O=C(NCCc1c[nH]c2ncccc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 16, 16, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337648445 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 Building ZINC000337648445 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337648445 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 207) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2ncccc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337648445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337648445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000337648445 none O=C(NCCc1c[nH]c2ncccc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 17, 17, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 208) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2ncccc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000337648445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337648445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000337648445 none O=C(NCCc1c[nH]c2ncccc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 16, 16, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337648445 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337648445 Building ZINC000337663061 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337663061 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/209 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O) `ZINC000337663061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337663061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337663061 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O 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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 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, 33, 33, 21, 33, 41, 41, 41, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 33, 33, 41, 41, 41, 41, 41, 41, 41, 41, 41, 33, 66] 90 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/210 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O) `ZINC000337663061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337663061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337663061 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O 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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 44, 44, 44, 34, 34, 34, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 68] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337663061 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 Building ZINC000337663061 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337663061 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 209) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O) `ZINC000337663061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337663061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337663061 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O 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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 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, 33, 33, 21, 33, 41, 41, 41, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 33, 33, 41, 41, 41, 41, 41, 41, 41, 41, 41, 33, 66] 90 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 210) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O) `ZINC000337663061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337663061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000337663061 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(C)(C)C)cc1O 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.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 34, 34, 34, 34, 44, 44, 44, 34, 34, 34, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 68] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337663061 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337663061 Building ZINC000337671442 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337671442 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/211 `/scratch/xiaobo/25650/xaq-8058115.17/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)NCCc2cccc3[nH]ccc32)cn1) `ZINC000337671442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337671442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337671442 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2cccc3[nH]ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 12, 12, 16, 16, 24, 24, 24, 24, 24, 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: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/212 `/scratch/xiaobo/25650/xaq-8058115.17/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)NCCc2cccc3[nH]ccc32)cn1) `ZINC000337671442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337671442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337671442 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2cccc3[nH]ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 12, 12, 17, 17, 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, 46]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337671442 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 Building ZINC000337671442 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337671442 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 211) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCCc2cccc3[nH]ccc32)cn1) `ZINC000337671442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337671442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337671442 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2cccc3[nH]ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 12, 12, 16, 16, 24, 24, 24, 24, 24, 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: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 212) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)NCCc2cccc3[nH]ccc32)cn1) `ZINC000337671442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337671442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337671442 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2cccc3[nH]ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 12, 12, 17, 17, 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, 46]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337671442 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337671442 Building ZINC000337734144 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337734144 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/213 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1) `ZINC000337734144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337734144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337734144 none Cn1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/214 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1) `ZINC000337734144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337734144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337734144 none Cn1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337734144 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 Building ZINC000337734144 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337734144 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 213) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1) `ZINC000337734144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337734144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337734144 none Cn1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 214) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1) `ZINC000337734144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337734144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000337734144 none Cn1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337734144 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337734144 Building ZINC000337829536 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337829536 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/215 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)C2)cc1) `ZINC000337829536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337829536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829536 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 15, 19, 26, 26, 26, 26, 26, 46, 26, 46, 46, 28, 46, 46, 26, 3, 3, 3, 3, 3, 3, 3, 26, 26, 26, 26, 26, 26, 46, 46, 138, 46, 46, 31, 46, 46, 26, 26, 3, 3] 150 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]) total number of confs: 378 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/216 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)C2)cc1) `ZINC000337829536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337829536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829536 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 14, 18, 31, 31, 31, 31, 31, 44, 31, 47, 47, 34, 47, 47, 31, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31, 44, 44, 132, 47, 47, 39, 47, 47, 31, 31, 3, 3] 150 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]) total number of confs: 341 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337829536 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 Building ZINC000337829536 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337829536 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 215) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)C2)cc1) `ZINC000337829536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337829536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829536 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 15, 19, 26, 26, 26, 26, 26, 46, 26, 46, 46, 28, 46, 46, 26, 3, 3, 3, 3, 3, 3, 3, 26, 26, 26, 26, 26, 26, 46, 46, 138, 46, 46, 31, 46, 46, 26, 26, 3, 3] 150 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]) total number of confs: 378 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 216) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)C2)cc1) `ZINC000337829536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337829536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829536 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 14, 18, 31, 31, 31, 31, 31, 44, 31, 47, 47, 34, 47, 47, 31, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31, 44, 44, 132, 47, 47, 39, 47, 47, 31, 31, 3, 3] 150 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]) total number of confs: 341 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337829536 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829536 Building ZINC000337829538 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337829538 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/217 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)C2)cc1) `ZINC000337829538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337829538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829538 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 2, 1, 1, 1, 2, 12, 15, 27, 27, 27, 27, 27, 44, 27, 50, 50, 50, 50, 50, 27, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27, 44, 44, 132, 50, 50, 50, 50, 50, 27, 27, 2, 2] 150 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]) total number of confs: 323 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/218 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)C2)cc1) `ZINC000337829538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337829538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829538 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 2, 1, 1, 1, 2, 12, 16, 28, 28, 28, 28, 28, 42, 28, 47, 47, 31, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 42, 42, 126, 47, 47, 31, 47, 47, 28, 28, 2, 2] 150 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]) total number of confs: 328 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337829538 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 Building ZINC000337829538 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337829538 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 217) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)C2)cc1) `ZINC000337829538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337829538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829538 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 2, 1, 1, 1, 2, 12, 15, 27, 27, 27, 27, 27, 44, 27, 50, 50, 50, 50, 50, 27, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27, 44, 44, 132, 50, 50, 50, 50, 50, 27, 27, 2, 2] 150 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]) total number of confs: 323 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 218) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)C2)cc1) `ZINC000337829538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337829538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000337829538 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@](CO)(c3ccccc3)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 2, 1, 1, 1, 2, 12, 16, 28, 28, 28, 28, 28, 42, 28, 47, 47, 31, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 42, 42, 126, 47, 47, 31, 47, 47, 28, 28, 2, 2] 150 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]) total number of confs: 328 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337829538 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337829538 Building ZINC000337881280 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337881280 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/219 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337881280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881280 none O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 17, 29, 29, 29, 29, 29, 44, 29, 47, 47, 34, 47, 47, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 44, 44, 132, 47, 47, 39, 47, 47, 29, 29, 3, 3, 3, 3] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 344 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/220 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337881280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881280 none O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 20, 28, 28, 28, 28, 28, 44, 28, 48, 48, 29, 48, 48, 28, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 28, 44, 44, 132, 48, 48, 32, 48, 48, 28, 28, 3, 3, 3, 3] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 342 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337881280 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 Building ZINC000337881280 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337881280 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 219) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337881280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881280 none O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 17, 29, 29, 29, 29, 29, 44, 29, 47, 47, 34, 47, 47, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 44, 44, 132, 47, 47, 39, 47, 47, 29, 29, 3, 3, 3, 3] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 344 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 220) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337881280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881280 none O=C(N1CCC[C@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 20, 28, 28, 28, 28, 28, 44, 28, 48, 48, 29, 48, 48, 28, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 28, 44, 44, 132, 48, 48, 32, 48, 48, 28, 28, 3, 3, 3, 3] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 342 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337881280 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881280 Building ZINC000337881406 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337881406 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/221 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337881406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881406 none O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 16, 30, 30, 30, 30, 30, 45, 30, 47, 47, 47, 47, 47, 30, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 135, 47, 47, 47, 47, 47, 30, 30, 2, 2, 2, 2] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/222 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337881406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881406 none O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 16, 29, 29, 29, 29, 29, 47, 29, 50, 50, 35, 50, 50, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 29, 29, 29, 29, 29, 29, 47, 47, 141, 50, 50, 34, 50, 50, 29, 29, 2, 2, 2, 2] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337881406 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 Building ZINC000337881406 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337881406 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 221) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337881406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881406 none O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 16, 30, 30, 30, 30, 30, 45, 30, 47, 47, 47, 47, 47, 30, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 135, 47, 47, 47, 47, 47, 30, 30, 2, 2, 2, 2] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 222) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337881406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337881406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337881406 none O=C(N1CCC[C@@](CO)(c2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 16, 29, 29, 29, 29, 29, 47, 29, 50, 50, 35, 50, 50, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 29, 29, 29, 29, 29, 29, 47, 47, 141, 50, 50, 34, 50, 50, 29, 29, 2, 2, 2, 2] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337881406 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337881406 Building ZINC000565315111 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565315111 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/223 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565315111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315111 none Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 9, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/224 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565315111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315111 none Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 9, 9, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000565315111 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 Building ZINC000565315111 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565315111 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 223) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565315111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315111 none Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 9, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 9, 9, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 224) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565315111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315111 none Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 9, 9, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000565315111 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315111 Building ZINC000565315113 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565315113 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/225 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565315113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315113 none Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 10, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 35] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/226 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565315113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315113 none Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 8, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 8, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000565315113 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 Building ZINC000565315113 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565315113 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 225) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565315113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315113 none Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 10, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 35] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 226) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1) `ZINC000565315113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565315113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000565315113 none Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 8, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 8, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000565315113 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565315113 Building ZINC000337969926 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337969926 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/227 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/227' -> `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(F)cc1) `ZINC000337969926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337969926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969926 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 28, 28, 28, 28, 28, 28, 6, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/228 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/228' -> `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(F)cc1) `ZINC000337969926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337969926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969926 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [42, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 28, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 42, 42, 42, 28, 28, 28, 28, 28, 28, 7, 6, 6, 6, 6] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337969926 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 Building ZINC000337969926 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337969926 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 227) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337969926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337969926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969926 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 28, 28, 28, 28, 28, 28, 6, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 228) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337969926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337969926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969926 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [42, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 28, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 42, 42, 42, 28, 28, 28, 28, 28, 28, 7, 6, 6, 6, 6] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337969926 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969926 Building ZINC000337969929 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337969929 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/229 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/229' -> `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(F)cc1) `ZINC000337969929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337969929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969929 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [45, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 25, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/230 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/230' -> `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(F)cc1) `ZINC000337969929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337969929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969929 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [47, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 28, 28, 28, 28, 28, 28, 6, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337969929 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 Building ZINC000337969929 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000337969929 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 229) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337969929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000337969929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969929 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [45, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 25, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 45, 45, 45, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 230) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000337969929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000337969929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000337969929 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [47, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 28, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 47, 47, 47, 28, 28, 28, 28, 28, 28, 6, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000337969929 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000337969929 Building ZINC000338033430 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338033430 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/231 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1) `ZINC000338033430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338033430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338033430 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 18, 18, 14, 18, 18, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 4, 9, 9, 18, 18, 14, 18, 18, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/232 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1) `ZINC000338033430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338033430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338033430 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 17, 10, 10, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 17, 17, 9, 17, 17, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 4, 9, 9, 17, 17, 9, 17, 17, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338033430 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 Building ZINC000338033430 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338033430 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 231) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1) `ZINC000338033430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338033430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338033430 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 10, 10, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 18, 18, 14, 18, 18, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 4, 9, 9, 18, 18, 14, 18, 18, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 232) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1) `ZINC000338033430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338033430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338033430 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nccn2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 17, 10, 10, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 17, 17, 9, 17, 17, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 4, 9, 9, 17, 17, 9, 17, 17, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338033430 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338033430 Building ZINC000180951058 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180951058 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/233 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CCO)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000180951058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180951058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000180951058 none Cc1ccc(CN(CCO)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 1 hydrogens 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, 18, 18, 18, 15, 6, 2, 6, 11, 13, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 15, 15, 11, 11, 13, 13, 39, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/234 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(CCO)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000180951058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180951058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000180951058 none Cc1ccc(CN(CCO)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 18, 18, 16, 6, 2, 6, 12, 13, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 16, 16, 12, 12, 13, 13, 39, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180951058 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 Building ZINC000180951058 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180951058 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 233) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(CN(CCO)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000180951058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180951058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000180951058 none Cc1ccc(CN(CCO)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 1 hydrogens 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, 18, 18, 18, 15, 6, 2, 6, 11, 13, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 15, 15, 11, 11, 13, 13, 39, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 234) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(CN(CCO)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000180951058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180951058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000180951058 none Cc1ccc(CN(CCO)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 18, 18, 16, 6, 2, 6, 12, 13, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 16, 16, 12, 12, 13, 13, 39, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000180951058 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000180951058 Building ZINC000338055743 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338055743 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/235 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338055743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055743 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 7, 8, 20, 20, 12, 20, 20, 20, 20, 8, 8, 8, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/236 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338055743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055743 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 15, 15, 15, 8, 8, 18, 18, 8, 18, 18, 18, 18, 8, 8, 8, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 18, 18, 18] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338055743 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 Building ZINC000338055743 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338055743 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 235) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338055743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055743 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 7, 8, 20, 20, 12, 20, 20, 20, 20, 8, 8, 8, 4, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 236) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338055743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055743 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 15, 15, 15, 8, 8, 18, 18, 8, 18, 18, 18, 18, 8, 8, 8, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 18, 18, 18] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338055743 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055743 Building ZINC000338055745 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338055745 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/237 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338055745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055745 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 7, 8, 18, 18, 12, 18, 18, 18, 18, 8, 8, 8, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 18, 18, 18] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/238 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338055745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055745 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 16, 16, 16, 8, 8, 17, 17, 9, 17, 17, 17, 17, 8, 8, 8, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338055745 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 Building ZINC000338055745 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338055745 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 237) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338055745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055745 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 7, 8, 18, 18, 12, 18, 18, 18, 18, 8, 8, 8, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 18, 18, 18] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 238) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000338055745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338055745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338055745 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 16, 16, 16, 8, 8, 17, 17, 9, 17, 17, 17, 17, 8, 8, 8, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338055745 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338055745 Building ZINC000912492772 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000912492772 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/239 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/240 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/241 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/241' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/242 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/242' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000912492772 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 Building ZINC000912492772 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000912492772 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 239) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 240) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 241) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 242) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000912492772 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 Building ZINC000912492772 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000912492772 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 239) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 240) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 241) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 242) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000912492772 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 Building ZINC000912492772 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000912492772 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 239) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 240) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 49, 49, 27, 27] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 241) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 242) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1) `ZINC000912492772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000912492772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000912492772 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H]1CCN(CC(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 10, 5, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 29, 29, 29, 29, 29, 49, 49, 49, 49, 29, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 49, 49, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 212 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000912492772 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000912492772 Building ZINC000338057902 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338057902 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/243 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCc2ccccc2OC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338057902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338057902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338057902 none O=C(N[C@@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 25, 25, 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, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/244 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCc2ccccc2OC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338057902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338057902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338057902 none O=C(N[C@@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338057902 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 Building ZINC000338057902 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338057902 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 243) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1CCc2ccccc2OC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338057902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338057902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338057902 none O=C(N[C@@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 25, 25, 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, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 244) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1CCc2ccccc2OC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338057902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338057902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338057902 none O=C(N[C@@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338057902 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338057902 Building ZINC000338058645 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338058645 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/245 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCc2ccccc2OC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338058645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338058645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338058645 none O=C(N[C@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 27, 27, 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, 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/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/246 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCc2ccccc2OC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338058645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338058645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338058645 none O=C(N[C@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338058645 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 Building ZINC000338058645 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338058645 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 245) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N[C@H]1CCc2ccccc2OC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338058645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338058645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338058645 none O=C(N[C@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 27, 27, 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, 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/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 246) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N[C@H]1CCc2ccccc2OC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338058645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338058645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338058645 none O=C(N[C@H]1CCc2ccccc2OC1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 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, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338058645 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338058645 Building ZINC000338053444 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338053444 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/247 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1) `ZINC000338053444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338053444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000338053444 none COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 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: [36, 36, 25, 36, 11, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 11, 11, 36, 36, 36, 25, 25, 4, 7, 7, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/248 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1) `ZINC000338053444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338053444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000338053444 none COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 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: [40, 40, 28, 40, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 40, 40, 40, 28, 28, 4, 6, 6, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338053444 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 Building ZINC000338053444 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338053444 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 247) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1) `ZINC000338053444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338053444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000338053444 none COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 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: [36, 36, 25, 36, 11, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 11, 11, 36, 36, 36, 25, 25, 4, 7, 7, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 248) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1) `ZINC000338053444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338053444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000338053444 none COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 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, 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: [40, 40, 28, 40, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 40, 40, 40, 28, 28, 4, 6, 6, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338053444 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338053444 Building ZINC000338054723 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338054723 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/249 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338054723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054723 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/250 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338054723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054723 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338054723 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 Building ZINC000338054723 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338054723 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 249) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338054723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054723 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 250) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338054723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054723 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338054723 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054723 Building ZINC000338054725 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338054725 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/251 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338054725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054725 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 6, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/252 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338054725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054725 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 6, 7, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338054725 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 Building ZINC000338054725 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338054725 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 251) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338054725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054725 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 6, 7, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 252) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1) `ZINC000338054725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338054725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338054725 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 6, 7, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338054725 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338054725 Building ZINC000338081556 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338081556 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/253 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1) `ZINC000338081556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338081556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000338081556 none Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 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, 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: [17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 19, 19, 19, 9, 17, 17, 17, 17, 17, 17, 17, 17, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 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, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/254 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1) `ZINC000338081556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338081556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000338081556 none Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 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, 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: [17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 18, 18, 18, 8, 17, 17, 17, 17, 17, 17, 17, 17, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 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, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338081556 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 Building ZINC000338081556 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338081556 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 253) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1) `ZINC000338081556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338081556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000338081556 none Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 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, 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: [17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 19, 19, 19, 9, 17, 17, 17, 17, 17, 17, 17, 17, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 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, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 254) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1) `ZINC000338081556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338081556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000338081556 none Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 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, 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: [17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 18, 18, 18, 8, 17, 17, 17, 17, 17, 17, 17, 17, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 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, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338081556 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338081556 Building ZINC000338092897 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338092897 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/255 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C) `ZINC000338092897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338092897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338092897 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C 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.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.3', '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, 5, 15, 15, 15, 8, 1, 5, 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, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 25, 25, 25, 25, 25] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/256 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C) `ZINC000338092897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338092897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338092897 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C 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.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.3', '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, 5, 15, 15, 15, 8, 1, 5, 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, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 25, 25, 25, 25, 25] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338092897 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 Building ZINC000338092897 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338092897 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 255) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C) `ZINC000338092897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338092897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338092897 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C 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.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.3', '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, 5, 15, 15, 15, 8, 1, 5, 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, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 25, 25, 25, 25, 25] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 256) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C) `ZINC000338092897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338092897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338092897 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(F)(F)F)nc1C 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.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.3', '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, 5, 15, 15, 15, 8, 1, 5, 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, 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] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 25, 25, 25, 25, 25] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338092897 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338092897 Building ZINC000338082171 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338082171 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/257 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(F)(F)F)C2)cn1) `ZINC000338082171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338082171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338082171 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(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', 'C.3', 'H', '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, 5, 7, 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: [15, 9, 15, 15, 9, 9, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 14, 14, 14, 14, 14, 14, 14, 14, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/258 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(F)(F)F)C2)cn1) `ZINC000338082171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338082171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338082171 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(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', 'C.3', 'H', '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, 5, 7, 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: [14, 8, 14, 14, 8, 8, 1, 1, 1, 2, 5, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 18, 18, 18, 18, 18, 18, 18, 18, 8] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338082171 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 Building ZINC000338082171 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338082171 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 257) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(F)(F)F)C2)cn1) `ZINC000338082171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338082171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338082171 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(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', 'C.3', 'H', '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, 5, 7, 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: [15, 9, 15, 15, 9, 9, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 14, 14, 14, 14, 14, 14, 14, 14, 9] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 258) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(F)(F)F)C2)cn1) `ZINC000338082171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338082171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000338082171 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C(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', 'C.3', 'H', '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, 5, 7, 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: [14, 8, 14, 14, 8, 8, 1, 1, 1, 2, 5, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 18, 18, 18, 18, 18, 18, 18, 18, 8] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338082171 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338082171 Building ZINC000338083047 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338083047 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/259 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338083047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083047 none COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 14, 14, 14, 24, 24, 24, 14, 14, 6, 6, 6, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/260 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338083047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083047 none COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 13, 13, 13, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 22, 22, 22, 13, 13, 5, 5, 5, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338083047 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 Building ZINC000338083047 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338083047 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 259) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338083047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083047 none COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 14, 14, 14, 24, 24, 24, 14, 14, 6, 6, 6, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 260) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338083047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083047 none COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 13, 13, 13, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 22, 22, 22, 13, 13, 5, 5, 5, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338083047 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083047 Building ZINC000338083049 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338083049 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/261 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338083049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083049 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 20, 20, 20, 12, 12, 5, 5, 5, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/262 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338083049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083049 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 25, 25, 25, 13, 13, 5, 5, 5, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338083049 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 Building ZINC000338083049 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338083049 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 261) grep: /scratch/xiaobo/25650/xaq-8058115.17/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([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338083049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083049 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 12, 12, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 20, 20, 20, 12, 12, 5, 5, 5, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 262) grep: /scratch/xiaobo/25650/xaq-8058115.17/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([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000338083049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338083049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338083049 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 25, 25, 25, 13, 13, 5, 5, 5, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/25650/xaq-8058115.17/working/building/ZINC000338083049 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338083049 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338083049 Building ZINC000338089553 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338089553 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/263 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1) `ZINC000338089553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338089553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089553 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 10, 13, 13, 13, 13, 38, 38, 38, 48, 48, 48, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/264 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1) `ZINC000338089553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338089553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089553 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 10, 15, 15, 15, 15, 39, 39, 39, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338089553 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 Building ZINC000338089553 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338089553 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 263) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1) `ZINC000338089553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338089553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089553 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 10, 13, 13, 13, 13, 38, 38, 38, 48, 48, 48, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 264) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1) `ZINC000338089553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338089553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089553 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 10, 15, 15, 15, 15, 39, 39, 39, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/25650/xaq-8058115.17/working/building/ZINC000338089553 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338089553 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089553 Building ZINC000338089555 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338089555 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/265 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1) `ZINC000338089555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338089555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089555 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 9, 15, 15, 15, 15, 34, 34, 34, 47, 47, 47, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 34, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/266 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1) `ZINC000338089555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338089555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089555 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 10, 16, 16, 16, 16, 34, 34, 34, 48, 48, 48, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 34, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338089555 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 Building ZINC000338089555 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338089555 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 265) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1) `ZINC000338089555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338089555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089555 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 9, 15, 15, 15, 15, 34, 34, 34, 47, 47, 47, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 34, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 266) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1) `ZINC000338089555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338089555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338089555 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N[C@H](C)C(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 4, 10, 16, 16, 16, 16, 34, 34, 34, 48, 48, 48, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 34, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 51, 52, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338089555 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338089555 Building ZINC000338102361 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338102361 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/267 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/267' -> `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])c1ccccc1OC) `ZINC000338102361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338102361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102361 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 28, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 9, 38, 38, 38, 28, 28, 28, 28, 28, 28, 8, 7, 7, 7, 7, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/268 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/268' -> `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])c1ccccc1OC) `ZINC000338102361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338102361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102361 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 28, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 8, 39, 39, 39, 28, 28, 28, 28, 28, 28, 8, 7, 7, 7, 7, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338102361 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 Building ZINC000338102361 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338102361 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 267) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000338102361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338102361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102361 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 28, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 9, 38, 38, 38, 28, 28, 28, 28, 28, 28, 8, 7, 7, 7, 7, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 268) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000338102361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338102361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102361 none COc1cc2c(cc1F)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 28, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 8, 39, 39, 39, 28, 28, 28, 28, 28, 28, 8, 7, 7, 7, 7, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338102361 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102361 Building ZINC000338102364 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338102364 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/269 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/269' -> `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])c1ccccc1OC) `ZINC000338102364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338102364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102364 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 25, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 7, 36, 36, 36, 28, 28, 28, 28, 28, 28, 8, 6, 6, 6, 6, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/270 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/270' -> `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])c1ccccc1OC) `ZINC000338102364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338102364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102364 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 25, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 39, 39, 39, 28, 28, 28, 28, 28, 28, 8, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338102364 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 Building ZINC000338102364 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338102364 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 269) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000338102364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338102364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102364 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 25, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 7, 36, 36, 36, 28, 28, 28, 28, 28, 28, 8, 6, 6, 6, 6, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 270) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000338102364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338102364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338102364 none COc1cc2c(cc1F)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC 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', '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, 1, 1, 15, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 25, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 39, 39, 39, 28, 28, 28, 28, 28, 28, 8, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338102364 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338102364 Building ZINC000338104204 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338104204 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/271 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000338104204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338104204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338104204 none COC(=O)c1c(F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 29, 6, 35, 6, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 19, 19, 19, 38, 37, 38, 19, 6, 5, 5, 5, 5, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/272 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000338104204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338104204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338104204 none COC(=O)c1c(F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 31, 6, 34, 6, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 34, 34, 34, 20, 6, 5, 5, 5, 5, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338104204 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 Building ZINC000338104204 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338104204 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 271) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000338104204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338104204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338104204 none COC(=O)c1c(F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 29, 6, 35, 6, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 19, 19, 19, 38, 37, 38, 19, 6, 5, 5, 5, 5, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 272) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F) `ZINC000338104204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338104204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338104204 none COC(=O)c1c(F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 31, 6, 34, 6, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 34, 34, 34, 20, 6, 5, 5, 5, 5, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338104204 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338104204 Building ZINC000338124138 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338124138 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/273 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000338124138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338124138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000338124138 none Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 31, 31, 31, 31, 31, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 31, 31, 31, 31, 6, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/274 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000338124138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338124138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000338124138 none Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 31, 31, 31, 31, 31, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 31, 31, 31, 31, 6, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338124138 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 Building ZINC000338124138 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338124138 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 273) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000338124138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338124138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000338124138 none Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 31, 31, 31, 31, 31, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 31, 31, 31, 31, 6, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 274) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000338124138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338124138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000338124138 none Cc1ccc(Cc2ccccn2)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 31, 31, 31, 31, 31, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 31, 31, 31, 31, 6, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338124138 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338124138 Building ZINC000338175611 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338175611 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/275 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@]2(CCc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338175611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175611 none O=C(N1CCO[C@@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 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: [11, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4] 38 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/276 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@]2(CCc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338175611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175611 none O=C(N1CCO[C@@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5] 41 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338175611 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 Building ZINC000338175611 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338175611 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 275) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@]2(CCc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338175611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175611 none O=C(N1CCO[C@@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 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: [11, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4] 38 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 276) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@]2(CCc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338175611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175611 none O=C(N1CCO[C@@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5] 41 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338175611 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175611 Building ZINC000338175614 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338175614 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/277 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@]2(CCc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338175614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175614 none O=C(N1CCO[C@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 28, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 4, 4, 1, 1, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4] 44 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/278 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@]2(CCc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338175614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175614 none O=C(N1CCO[C@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [14, 2, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 5, 5, 1, 1, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5] 44 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338175614 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 Building ZINC000338175614 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338175614 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 277) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCO[C@]2(CCc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338175614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175614 none O=C(N1CCO[C@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 28, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 4, 4, 1, 1, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4] 44 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 278) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCO[C@]2(CCc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338175614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338175614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000338175614 none O=C(N1CCO[C@]2(CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [14, 2, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 5, 5, 1, 1, 5, 5, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5] 44 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338175614 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338175614 Building ZINC000338233673 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338233673 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/279 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1) `ZINC000338233673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338233673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338233673 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 11, 24, 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] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/280 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1) `ZINC000338233673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338233673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338233673 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338233673 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 Building ZINC000338233673 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338233673 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 279) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1) `ZINC000338233673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338233673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338233673 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 11, 24, 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] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 280) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1) `ZINC000338233673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338233673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338233673 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCOc2cccc(F)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338233673 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338233673 Building ZINC000338234105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338234105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/281 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOCc1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338234105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338234105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000338234105 none O=C(NCCOCc1ccc(Cl)cc1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations 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, 10, 23, 48, 50, 50, 48, 48, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 10, 10, 48, 48, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/282 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOCc1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338234105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338234105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000338234105 none O=C(NCCOCc1ccc(Cl)cc1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations 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, 11, 24, 49, 50, 50, 49, 49, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 11, 11, 49, 49, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338234105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 Building ZINC000338234105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338234105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 281) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCOCc1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338234105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338234105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000338234105 none O=C(NCCOCc1ccc(Cl)cc1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations 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, 10, 23, 48, 50, 50, 48, 48, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 10, 10, 48, 48, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 282) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCOCc1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338234105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338234105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000338234105 none O=C(NCCOCc1ccc(Cl)cc1)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 conformations 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, 11, 24, 49, 50, 50, 49, 49, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 11, 11, 49, 49, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338234105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338234105 Building ZINC000338240953 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338240953 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/283 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cccc(F)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338240953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338240953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000338240953 none O=C(N1CCOc2cccc(F)c2C1)[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', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 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/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/284 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2cccc(F)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338240953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338240953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000338240953 none O=C(N1CCOc2cccc(F)c2C1)[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', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338240953 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 Building ZINC000338240953 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338240953 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 283) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCOc2cccc(F)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338240953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338240953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000338240953 none O=C(N1CCOc2cccc(F)c2C1)[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', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 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/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 284) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCOc2cccc(F)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338240953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338240953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000338240953 none O=C(N1CCOc2cccc(F)c2C1)[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', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338240953 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338240953 Building ZINC000181226185 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181226185 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/285 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226185 none O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 6, 11, 11, 11, 11, 11, 11, 28, 29, 29, 29, 29, 29, 11, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 11, 11, 11, 11, 28, 28, 29, 29, 28, 29, 29, 11, 11, 5, 7, 7, 7, 7, 7, 7, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/286 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226185 none O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 13, 13, 26, 27, 27, 26, 27, 27, 13, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 13, 13, 13, 13, 26, 26, 27, 27, 26, 27, 27, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181226185 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 Building ZINC000181226185 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181226185 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 285) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226185 none O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 6, 11, 11, 11, 11, 11, 11, 28, 29, 29, 29, 29, 29, 11, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 11, 11, 11, 11, 28, 28, 29, 29, 28, 29, 29, 11, 11, 5, 7, 7, 7, 7, 7, 7, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 286) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181226185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226185 none O=C(N1CCO[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 13, 13, 26, 27, 27, 26, 27, 27, 13, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 13, 13, 13, 13, 26, 26, 27, 27, 26, 27, 27, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181226185 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226185 Building ZINC000181226200 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181226200 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/287 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226200 none O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 13, 13, 26, 27, 27, 27, 27, 27, 13, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 13, 13, 13, 13, 26, 26, 27, 27, 27, 27, 27, 13, 13, 5, 7, 7, 7, 7, 7, 7, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/288 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226200 none O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 12, 12, 12, 27, 28, 28, 27, 28, 28, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 27, 27, 28, 28, 27, 28, 28, 12, 12, 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, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181226200 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 Building ZINC000181226200 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181226200 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 287) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226200 none O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 13, 13, 26, 27, 27, 27, 27, 27, 13, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 13, 13, 13, 13, 26, 26, 27, 27, 27, 27, 27, 13, 13, 5, 7, 7, 7, 7, 7, 7, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 288) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000181226200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181226200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000181226200 none O=C(N1CCO[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 12, 12, 12, 27, 28, 28, 27, 28, 28, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 27, 27, 28, 28, 27, 28, 28, 12, 12, 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, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000181226200 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000181226200 Building ZINC000338314605 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338314605 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/289 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CCO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338314605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338314605 none CCC(CC)(CCO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 5, 13, 28, 13, 35, 37, 5, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 35, 35, 37, 37, 111, 5, 4, 4, 4, 4] 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]) total number of confs: 448 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/290 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CCO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338314605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338314605 none CCC(CC)(CCO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 13, 5, 13, 29, 13, 35, 37, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 35, 35, 37, 37, 111, 5, 4, 4, 4, 4] 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]) total number of confs: 450 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338314605 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 Building ZINC000338314605 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338314605 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 289) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC(CC)(CCO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338314605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338314605 none CCC(CC)(CCO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 5, 13, 28, 13, 35, 37, 5, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 35, 35, 37, 37, 111, 5, 4, 4, 4, 4] 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]) total number of confs: 448 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 290) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC(CC)(CCO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338314605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338314605 none CCC(CC)(CCO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 13, 5, 13, 29, 13, 35, 37, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 35, 35, 37, 37, 111, 5, 4, 4, 4, 4] 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]) total number of confs: 450 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338314605 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338314605 Building ZINC000338381261 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338381261 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/291 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCc1nccs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000338381261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338381261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000338381261 none CC(C)N(CCc1nccs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 8, 1, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 2, 6, 11, 11, 25, 25, 25, 25, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 25, 25, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/292 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCc1nccs1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000338381261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338381261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000338381261 none CC(C)N(CCc1nccs1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 8, 1, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 2, 6, 10, 10, 24, 24, 24, 24, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 24, 24, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338381261 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 Building ZINC000338381261 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338381261 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 291) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)N(CCc1nccs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000338381261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338381261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000338381261 none CC(C)N(CCc1nccs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 8, 1, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 2, 6, 11, 11, 25, 25, 25, 25, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 25, 25, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 292) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)N(CCc1nccs1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000338381261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338381261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000338381261 none CC(C)N(CCc1nccs1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 8, 1, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 2, 6, 10, 10, 24, 24, 24, 24, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 24, 24, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338381261 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338381261 Building ZINC000338492079 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338492079 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/293 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338492079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338492079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000338492079 none Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 4, 4, 1, 3, 4, 4, 46, 46, 46, 46, 46, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/294 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338492079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338492079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000338492079 none Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338492079 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 Building ZINC000338492079 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338492079 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 293) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338492079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338492079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000338492079 none Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 4, 4, 1, 3, 4, 4, 46, 46, 46, 46, 46, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 294) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338492079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338492079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000338492079 none Cn1nccc1C1=C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338492079 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338492079 Building ZINC000338493719 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338493719 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/295 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338493719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493719 none CC1(C)SC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 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, 36, 36, 36, 36, 18, 36, 10, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 10, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/296 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338493719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493719 none CC1(C)SC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 33, 16, 33, 9, 1, 9, 1, 1, 1, 6, 6, 1, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 9, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338493719 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 Building ZINC000338493719 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338493719 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 295) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC1(C)SC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338493719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493719 none CC1(C)SC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 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, 36, 36, 36, 36, 18, 36, 10, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 10, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 296) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC1(C)SC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338493719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493719 none CC1(C)SC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 33, 16, 33, 9, 1, 9, 1, 1, 1, 6, 6, 1, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 9, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338493719 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493719 Building ZINC000338493720 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338493720 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/297 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338493720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493720 none CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 32, 14, 32, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 7, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/298 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338493720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493720 none CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 20, 38, 10, 1, 10, 1, 1, 1, 6, 6, 1, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 10, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338493720 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 Building ZINC000338493720 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338493720 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 297) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338493720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493720 none CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 32, 14, 32, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 7, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 298) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338493720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338493720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000338493720 none CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 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, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 20, 38, 10, 1, 10, 1, 1, 1, 6, 6, 1, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 10, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338493720 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338493720 Building ZINC000338503748 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338503748 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/299 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338503748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503748 none C[C@@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 13, 13, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 26, 26, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/300 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338503748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503748 none C[C@@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 29, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 20, 13, 13, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 49, 50, 51, 52]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338503748 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 Building ZINC000338503748 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338503748 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 299) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338503748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503748 none C[C@@H]1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 13, 13, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 26, 26, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 300) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338503748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503748 none C[C@@H]1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 29, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 20, 13, 13, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 49, 50, 51, 52]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338503748 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503748 Building ZINC000338503749 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338503749 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/301 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1) `ZINC000338503749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338503749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503749 none C[C@@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 20, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/302 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1) `ZINC000338503749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338503749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503749 none C[C@@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 21, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 14, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338503749 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 Building ZINC000338503749 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338503749 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 301) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1) `ZINC000338503749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338503749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503749 none C[C@@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 20, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 14, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 302) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1) `ZINC000338503749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338503749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503749 none C[C@@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 21, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 14, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338503749 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503749 Building ZINC000338503750 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338503750 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/303 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338503750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503750 none C[C@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 20, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 14, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/304 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338503750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503750 none C[C@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 19, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 13, 13, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338503750 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 Building ZINC000338503750 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338503750 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 303) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338503750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503750 none C[C@H]1CC(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 20, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 14, 14, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 304) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1) `ZINC000338503750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338503750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000338503750 none C[C@H]1CC(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 19, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 13, 13, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338503750 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338503750 Building ZINC000338509020 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338509020 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/305 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338509020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000338509020 none O=C(Nc1ccc(OC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 12, 12, 12, 25, 31, 31, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 31, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/306 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338509020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000338509020 none O=C(Nc1ccc(OC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 12, 12, 12, 25, 30, 30, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 30, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338509020 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 Building ZINC000338509020 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338509020 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 305) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(Nc1ccc(OC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338509020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000338509020 none O=C(Nc1ccc(OC(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 12, 12, 12, 25, 31, 31, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 31, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 306) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(Nc1ccc(OC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338509020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000338509020 none O=C(Nc1ccc(OC(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 12, 12, 12, 25, 30, 30, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 30, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338509020 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509020 Building ZINC000338509455 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338509455 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/307 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338509455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338509455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000338509455 none Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 41, 41, 41, 41, 41, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5] 45 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]) total number of confs: 72 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/308 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338509455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338509455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000338509455 none Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5] 46 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]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338509455 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 Building ZINC000338509455 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338509455 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 307) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338509455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338509455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000338509455 none Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 41, 41, 41, 41, 41, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5] 45 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]) total number of confs: 72 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 308) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338509455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338509455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000338509455 none Cn1nccc1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 8, 1, 1, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5] 46 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]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338509455 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338509455 Building ZINC000282542129 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282542129 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/309 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/310 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/311 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/311' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/312 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/312' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282542129 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 Building ZINC000282542129 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282542129 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 309) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 310) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 311) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 312) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282542129 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 Building ZINC000282542129 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282542129 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 309) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 310) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 311) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 312) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282542129 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 Building ZINC000282542129 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282542129 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 309) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 310) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 311) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 312) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1) `ZINC000282542129.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282542129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000282542129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(N2CCc3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 12, 12, 12, 12] 42 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282542129 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282542129 Building ZINC000282607215 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282607215 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/313 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282607215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607215 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 2, 8, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 11, 11, 11, 11, 11, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/314 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282607215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607215 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 2, 7, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282607215 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 Building ZINC000282607215 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282607215 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 313) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282607215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607215 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 2, 8, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 11, 11, 11, 11, 11, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4] 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 314) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282607215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607215 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 2, 7, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282607215 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607215 Building ZINC000282607217 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282607217 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/315 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282607217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607217 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 9, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 10, 10, 10, 10, 10, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/316 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282607217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607217 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 9, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282607217 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 Building ZINC000282607217 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282607217 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 315) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282607217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607217 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 3, 3, 1, 1, 1, 1, 9, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 10, 10, 10, 10, 10, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 316) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1) `ZINC000282607217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282607217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000282607217 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)C3(CCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 2, 9, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282607217 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282607217 Building ZINC000338609185 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338609185 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/317 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338609185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338609185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338609185 none O=C(NCc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 21, 21, 21, 21, 21, 26, 26, 21, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 21, 21, 26, 26, 21, 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, 44]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/318 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338609185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338609185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338609185 none O=C(NCc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 22, 22, 22, 22, 22, 28, 28, 22, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 22, 22, 28, 28, 22, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338609185 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 Building ZINC000338609185 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338609185 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 317) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338609185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338609185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338609185 none O=C(NCc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 21, 21, 21, 21, 21, 26, 26, 21, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 21, 21, 26, 26, 21, 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, 44]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 318) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000338609185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338609185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338609185 none O=C(NCc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 22, 22, 22, 22, 22, 28, 28, 22, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 22, 22, 28, 28, 22, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338609185 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338609185 Building ZINC000565954225 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565954225 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/319 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C) `ZINC000565954225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565954225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000565954225 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 44, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/320 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C) `ZINC000565954225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565954225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000565954225 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 40, 7, 40, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000565954225 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 Building ZINC000565954225 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565954225 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 319) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C) `ZINC000565954225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565954225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000565954225 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 44, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 320) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C) `ZINC000565954225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565954225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000565954225 none CCOC(=O)[C@@H]1CC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 40, 7, 40, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 7, 7, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000565954225 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000565954225 Building ZINC000338660719 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338660719 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/321 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000338660719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338660719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338660719 none CCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 8, 31, 31, 31, 31, 31, 27, 27, 2, 8, 8, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 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, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/322 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000338660719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338660719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338660719 none CCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 32, 32, 32, 32, 32, 25, 25, 2, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 46]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338660719 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 Building ZINC000338660719 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338660719 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 321) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000338660719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338660719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338660719 none CCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 8, 31, 31, 31, 31, 31, 27, 27, 2, 8, 8, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 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, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 322) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000338660719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338660719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338660719 none CCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 32, 32, 32, 32, 32, 25, 25, 2, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 46]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338660719 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338660719 Building ZINC000282694233 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282694233 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/323 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000282694233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282694233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694233 none O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 25, 1, 1, 1, 4, 4, 1, 4, 4, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 25, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/324 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000282694233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282694233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694233 none O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 3, 3, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282694233 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 Building ZINC000282694233 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282694233 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 323) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000282694233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282694233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694233 none O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 25, 1, 1, 1, 4, 4, 1, 4, 4, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 25, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 324) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000282694233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282694233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694233 none O=C(N1CCC[C@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 3, 3, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282694233 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694233 Building ZINC000282694237 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282694237 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/325 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000282694237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282694237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694237 none O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 3, 3, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 3, 3, 1, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/326 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000282694237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282694237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694237 none O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 23, 23, 23, 23, 23, 49, 49, 49, 49, 49, 49, 49, 49, 23, 1, 1, 1, 5, 5, 1, 5, 5, 23, 23, 23, 23, 23, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49, 23, 23, 5, 5, 2, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282694237 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 Building ZINC000282694237 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282694237 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 325) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000282694237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282694237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694237 none O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 3, 3, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 3, 3, 1, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 326) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000282694237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282694237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000282694237 none O=C(N1CCC[C@@H](c2ncc3n2CCCC3)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 23, 23, 23, 23, 23, 49, 49, 49, 49, 49, 49, 49, 49, 23, 1, 1, 1, 5, 5, 1, 5, 5, 23, 23, 23, 23, 23, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49, 23, 23, 5, 5, 2, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282694237 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282694237 Building ZINC000338645106 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338645106 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/327 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000338645106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338645106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338645106 none Cc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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: [28, 28, 28, 28, 28, 28, 28, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 28, 28, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/328 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000338645106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338645106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338645106 none Cc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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: [30, 30, 30, 30, 30, 30, 30, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 30, 30, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338645106 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 Building ZINC000338645106 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338645106 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 327) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000338645106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338645106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338645106 none Cc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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: [28, 28, 28, 28, 28, 28, 28, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 28, 28, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 328) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000338645106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338645106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338645106 none Cc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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: [30, 30, 30, 30, 30, 30, 30, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 30, 30, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338645106 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338645106 Building ZINC000338689336 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338689336 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/329 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1) `ZINC000338689336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338689336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338689336 none CC(C)c1nc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 24, 33, 24, 24, 13, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 24, 24, 33, 33, 33, 33, 33, 33, 33, 13, 13, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/330 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1) `ZINC000338689336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338689336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338689336 none CC(C)c1nc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 23, 34, 23, 23, 12, 7, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 23, 23, 34, 34, 34, 34, 34, 34, 34, 12, 12, 7, 7, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338689336 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 Building ZINC000338689336 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338689336 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 329) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1) `ZINC000338689336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338689336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338689336 none CC(C)c1nc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 24, 33, 24, 24, 13, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 24, 24, 33, 33, 33, 33, 33, 33, 33, 13, 13, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 330) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1nc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1) `ZINC000338689336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338689336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000338689336 none CC(C)c1nc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 23, 34, 23, 23, 12, 7, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 23, 23, 34, 34, 34, 34, 34, 34, 34, 12, 12, 7, 7, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338689336 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338689336 Building ZINC000471699052 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471699052 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/331 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21) `ZINC000471699052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471699052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000471699052 none Cn1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 15, 15, 3, 3, 3, 3, 3, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/332 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21) `ZINC000471699052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471699052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000471699052 none Cn1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 15, 15, 3, 3, 3, 3, 3, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471699052 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 Building ZINC000471699052 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471699052 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 331) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21) `ZINC000471699052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471699052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000471699052 none Cn1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 15, 15, 3, 3, 3, 3, 3, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 332) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21) `ZINC000471699052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471699052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000471699052 none Cn1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2ccc(F)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 15, 15, 3, 3, 3, 3, 3, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471699052 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471699052 Building ZINC000471700307 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471700307 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/333 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C)nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471700307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471700307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000471700307 none COc1ccc(C)nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 31, 31, 31, 31, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 40, 40, 40, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/334 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C)nc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471700307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471700307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000471700307 none COc1ccc(C)nc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 31, 31, 31, 31, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 40, 40, 40, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471700307 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 Building ZINC000471700307 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471700307 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 333) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(C)nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471700307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471700307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000471700307 none COc1ccc(C)nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 31, 31, 31, 31, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 40, 40, 40, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 334) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(C)nc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471700307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471700307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000471700307 none COc1ccc(C)nc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 31, 31, 31, 31, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 40, 40, 40, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471700307 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471700307 Building ZINC000282789871 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282789871 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/335 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/335' -> `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)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/336 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/336' -> `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)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/337 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/337' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 46, 46, 46, 46, 46, 47, 47, 47, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/338 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/338' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 46, 47, 47, 46, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282789871 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 Building ZINC000282789871 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282789871 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 335) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 336) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 337) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 46, 46, 46, 46, 46, 47, 47, 47, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 338) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 46, 47, 47, 46, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282789871 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 Building ZINC000282789871 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282789871 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 335) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 336) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 337) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 46, 46, 46, 46, 46, 47, 47, 47, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 338) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 46, 47, 47, 46, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282789871 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 Building ZINC000282789871 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282789871 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 335) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 336) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 337) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 46, 46, 46, 46, 46, 47, 47, 47, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 338) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NC[C@H]1C[C@@H](c2ccccc2)C1) `ZINC000282789871.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282789871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000282789871 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](c2ccccc2)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', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 46, 46, 46, 46, 46, 47, 47, 46, 47, 47, 46, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 46, 46, 47, 47, 47, 47, 47, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000282789871 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000282789871 Building ZINC000471878970 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471878970 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/339 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000471878970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471878970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000471878970 none CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 44, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 5, 9, 9, 9, 9, 9, 49, 49, 49, 49, 49, 16, 16, 3, 3, 3, 1, 3, 3, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/340 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000471878970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471878970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000471878970 none CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 17, 41, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 6, 9, 9, 6, 9, 9, 50, 50, 50, 50, 50, 17, 17, 3, 3, 3, 1, 3, 3, 9, 9, 6, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471878970 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 Building ZINC000471878970 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471878970 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 339) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000471878970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471878970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000471878970 none CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 44, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 5, 9, 9, 9, 9, 9, 49, 49, 49, 49, 49, 16, 16, 3, 3, 3, 1, 3, 3, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 340) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1) `ZINC000471878970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471878970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000471878970 none CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 17, 41, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 6, 9, 9, 6, 9, 9, 50, 50, 50, 50, 50, 17, 17, 3, 3, 3, 1, 3, 3, 9, 9, 6, 9, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471878970 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471878970 Building ZINC000471863658 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471863658 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/341 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2) `ZINC000471863658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471863658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000471863658 none COc1cc2c(cc1OC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 48, 23, 23, 9, 2, 12, 1, 1, 1, 3, 3, 1, 3, 3, 23, 23, 49, 49, 49, 23, 23, 48, 48, 48, 23, 23, 23, 23, 3, 3, 1, 3, 3, 23, 23, 23, 23] 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]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/342 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2) `ZINC000471863658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471863658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000471863658 none COc1cc2c(cc1OC)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 9, 2, 12, 1, 1, 1, 3, 3, 1, 3, 3, 25, 25, 49, 49, 49, 25, 25, 49, 49, 49, 25, 25, 25, 25, 3, 3, 1, 3, 3, 25, 25, 25, 25] 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]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471863658 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 Building ZINC000471863658 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471863658 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 341) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1OC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2) `ZINC000471863658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471863658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000471863658 none COc1cc2c(cc1OC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 48, 23, 23, 9, 2, 12, 1, 1, 1, 3, 3, 1, 3, 3, 23, 23, 49, 49, 49, 23, 23, 48, 48, 48, 23, 23, 23, 23, 3, 3, 1, 3, 3, 23, 23, 23, 23] 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]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 342) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc2c(cc1OC)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2) `ZINC000471863658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471863658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000471863658 none COc1cc2c(cc1OC)CCN(C(=O)[C@]([O-])([SiH3])c1ccccc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 25, 25, 25, 25, 25, 25, 25, 25, 49, 25, 25, 9, 2, 12, 1, 1, 1, 3, 3, 1, 3, 3, 25, 25, 49, 49, 49, 25, 25, 49, 49, 49, 25, 25, 25, 25, 3, 3, 1, 3, 3, 25, 25, 25, 25] 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]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000471863658 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000471863658 Building ZINC000190240448 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190240448 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/343 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000190240448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190240448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190240448 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens need 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, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 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, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/344 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000190240448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190240448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190240448 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens need 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, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 48, 48, 48, 48, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190240448 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 Building ZINC000190240448 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190240448 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 343) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000190240448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190240448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190240448 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens need 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, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 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, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 344) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCO[C@H]2c2ccccc2)cc1) `ZINC000190240448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190240448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190240448 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 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, 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, 7, 7, 7] 0 hydrogens need 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, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 13, 13, 48, 48, 48, 48, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190240448 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190240448 Building ZINC000338856938 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338856938 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/345 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cn(Cc2ccccc2)nn1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000338856938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338856938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338856938 none O=C(Nc1cn(Cc2ccccc2)nn1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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: [11, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 29, 36, 36, 31, 36, 36, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 3, 7, 29, 29, 36, 36, 36, 36, 36, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/346 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cn(Cc2ccccc2)nn1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000338856938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338856938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338856938 none O=C(Nc1cn(Cc2ccccc2)nn1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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: [11, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 30, 37, 37, 37, 37, 37, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 3, 7, 30, 30, 37, 37, 37, 37, 37, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338856938 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 Building ZINC000338856938 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338856938 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 345) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1cn(Cc2ccccc2)nn1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000338856938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338856938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338856938 none O=C(Nc1cn(Cc2ccccc2)nn1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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: [11, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 29, 36, 36, 31, 36, 36, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 3, 7, 29, 29, 36, 36, 36, 36, 36, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 346) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1cn(Cc2ccccc2)nn1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000338856938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338856938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000338856938 none O=C(Nc1cn(Cc2ccccc2)nn1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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: [11, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 30, 37, 37, 37, 37, 37, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 3, 7, 30, 30, 37, 37, 37, 37, 37, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338856938 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338856938 Building ZINC000338860001 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338860001 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/347 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1) `ZINC000338860001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338860001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338860001 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 43, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 43, 43, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/348 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1) `ZINC000338860001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338860001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338860001 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 44, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 44, 44, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338860001 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 Building ZINC000338860001 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338860001 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 347) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1) `ZINC000338860001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338860001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338860001 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 43, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 43, 43, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 348) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1) `ZINC000338860001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338860001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000338860001 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cn(Cc2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 44, 50, 50, 50, 50, 50, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 44, 44, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338860001 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338860001 Building ZINC000338869576 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338869576 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/349 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ncc(c2cccs2)[nH]1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338869576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338869576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000338869576 none O=C(NCc1ncc(c2cccs2)[nH]1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 6, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 12, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 12, 12, 22, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/350 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ncc(c2cccs2)[nH]1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338869576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338869576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000338869576 none O=C(NCc1ncc(c2cccs2)[nH]1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 6, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 12, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 12, 12, 22, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338869576 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 Building ZINC000338869576 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338869576 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 349) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(NCc1ncc(c2cccs2)[nH]1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338869576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338869576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000338869576 none O=C(NCc1ncc(c2cccs2)[nH]1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 6, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 12, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 12, 12, 22, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 350) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(NCc1ncc(c2cccs2)[nH]1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000338869576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338869576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000338869576 none O=C(NCc1ncc(c2cccs2)[nH]1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 6, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 12, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 12, 12, 22, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338869576 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338869576 Building ZINC000338870354 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338870354 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/351 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338870354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338870354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000338870354 none COCCC(C)(C)NC(=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', '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, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 36, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 44, 44, 44, 37, 37, 36, 36, 12, 12, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/352 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338870354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338870354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000338870354 none COCCC(C)(C)NC(=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', '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, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 36, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 44, 44, 37, 37, 36, 36, 12, 12, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338870354 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 Building ZINC000338870354 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338870354 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 351) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338870354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338870354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000338870354 none COCCC(C)(C)NC(=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', '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, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 36, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 44, 44, 44, 37, 37, 36, 36, 12, 12, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 352) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000338870354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338870354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000338870354 none COCCC(C)(C)NC(=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', '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, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 36, 12, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 44, 44, 37, 37, 36, 36, 12, 12, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338870354 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338870354 Building ZINC000338911978 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338911978 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/353 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338911978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911978 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/354 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338911978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911978 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338911978 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 Building ZINC000338911978 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338911978 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 353) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338911978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911978 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 354) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338911978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911978 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/25650/xaq-8058115.17/working/building/ZINC000338911978 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338911978 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911978 Building ZINC000338911980 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338911980 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/355 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338911980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911980 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 20, 20, 20, 20, 20, 20, 7, 7, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/356 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338911980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911980 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338911980 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 Building ZINC000338911980 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338911980 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 355) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338911980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911980 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 7, 20, 20, 20, 20, 20, 20, 7, 7, 7, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 356) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1) `ZINC000338911980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338911980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000338911980 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338911980 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338911980 Building ZINC000338920652 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338920652 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/357 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1) `ZINC000338920652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338920652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338920652 none CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 50, 32, 32, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 6, 5, 5, 5, 5, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/358 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1) `ZINC000338920652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338920652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338920652 none CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 50, 32, 32, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 6, 5, 5, 5, 5, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338920652 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 Building ZINC000338920652 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000338920652 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 357) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1) `ZINC000338920652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000338920652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338920652 none CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 50, 32, 32, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 6, 5, 5, 5, 5, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 358) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1) `ZINC000338920652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000338920652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000338920652 none CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 50, 32, 32, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 6, 5, 5, 5, 5, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000338920652 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000338920652 Building ZINC000182212833 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182212833 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/359 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1COC2(CCCCC2)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182212833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212833 none O=C(NC[C@@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 15, 15, 17, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/360 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1COC2(CCCCC2)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182212833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212833 none O=C(NC[C@@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 14, 14, 16, 27, 27, 27, 27, 27, 27, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182212833 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 Building ZINC000182212833 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182212833 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 359) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1COC2(CCCCC2)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182212833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212833 none O=C(NC[C@@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 15, 15, 17, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 15, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 360) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1COC2(CCCCC2)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182212833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212833 none O=C(NC[C@@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 14, 14, 16, 27, 27, 27, 27, 27, 27, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182212833 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212833 Building ZINC000182212854 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182212854 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/361 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1COC2(CCCCC2)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182212854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212854 none O=C(NC[C@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 15, 15, 28, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 17, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/362 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1COC2(CCCCC2)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182212854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212854 none O=C(NC[C@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 15, 15, 28, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 17, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182212854 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 Building ZINC000182212854 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182212854 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 361) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1COC2(CCCCC2)O1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182212854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212854 none O=C(NC[C@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 15, 15, 28, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 17, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 362) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1COC2(CCCCC2)O1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182212854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182212854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000182212854 none O=C(NC[C@H]1COC2(CCCCC2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 15, 15, 28, 28, 28, 28, 28, 28, 28, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 17, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182212854 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182212854 Building ZINC000339163338 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163338 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/363 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163338 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/364 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163338 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163338 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 Building ZINC000339163338 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163338 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 363) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163338 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 364) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163338 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163338 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163338 Building ZINC000339163340 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163340 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/365 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163340 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/366 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163340 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens 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, 3, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 3, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163340 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 Building ZINC000339163340 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163340 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 365) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163340 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 366) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163340 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens 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, 3, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 3, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163340 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163340 Building ZINC000339163342 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163342 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/367 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163342 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/368 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163342 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163342 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 Building ZINC000339163342 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163342 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 367) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163342 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 368) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21) `ZINC000339163342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163342 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163342 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163342 Building ZINC000339163343 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163343 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/369 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163343 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens 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, 3, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/370 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163343 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 28, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163343 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 Building ZINC000339163343 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339163343 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 369) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339163343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163343 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens 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, 3, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 370) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21) `ZINC000339163343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339163343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339163343 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H]1COc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 28, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339163343 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339163343 Building ZINC000339171321 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339171321 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/371 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339171321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339171321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000339171321 none CCOc1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 18, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 31, 31, 31, 31, 31, 8, 8, 8, 8, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/372 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339171321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339171321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000339171321 none CCOc1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 30, 30, 30, 30, 30, 7, 7, 7, 7, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339171321 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 Building ZINC000339171321 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339171321 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 371) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339171321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339171321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000339171321 none CCOc1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 18, 8, 8, 8, 8, 8, 8, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 31, 31, 31, 31, 31, 8, 8, 8, 8, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 372) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339171321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339171321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000339171321 none CCOc1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 30, 30, 30, 30, 30, 7, 7, 7, 7, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/25650/xaq-8058115.17/working/building/ZINC000339171321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339171321 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339171321 Building ZINC000182610767 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182610767 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/373 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nncn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182610767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182610767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000182610767 none O=C(Nc1nncn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 12, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12, 23, 23, 12, 23, 23, 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]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/374 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nncn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182610767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182610767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000182610767 none O=C(Nc1nncn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 21, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12, 23, 23, 22, 23, 23, 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]) total number of confs: 58 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182610767 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 Building ZINC000182610767 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182610767 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 373) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(Nc1nncn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182610767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182610767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000182610767 none O=C(Nc1nncn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 12, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12, 23, 23, 12, 23, 23, 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]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 374) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(Nc1nncn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000182610767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182610767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000182610767 none O=C(Nc1nncn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 21, 23, 23, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 12, 23, 23, 22, 23, 23, 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]) total number of confs: 58 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182610767 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182610767 Building ZINC000339180804 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339180804 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/375 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1) `ZINC000339180804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339180804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339180804 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 13, 13, 22, 22, 22, 22, 22, 22, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/376 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1) `ZINC000339180804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339180804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339180804 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 13, 13, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339180804 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 Building ZINC000339180804 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339180804 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 375) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1) `ZINC000339180804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339180804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339180804 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 13, 13, 22, 22, 22, 22, 22, 22, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 376) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1) `ZINC000339180804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339180804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339180804 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc3ccccc3n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 13, 13, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339180804 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339180804 Building ZINC000339199007 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339199007 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/377 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000339199007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339199007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339199007 none CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 8, 25, 24, 3, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 25, 25, 37, 37, 37, 37, 27, 27, 27, 27, 27, 25, 25, 25, 3, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/378 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000339199007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339199007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339199007 none CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 10, 30, 27, 3, 10, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 28, 28, 35, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 30, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339199007 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 Building ZINC000339199007 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339199007 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 377) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000339199007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339199007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339199007 none CC[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 8, 25, 24, 3, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 25, 25, 37, 37, 37, 37, 27, 27, 27, 27, 27, 25, 25, 25, 3, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 378) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000339199007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339199007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339199007 none CC[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 10, 30, 27, 3, 10, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 28, 28, 35, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 30, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339199007 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339199007 Building ZINC000339193848 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193848 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/379 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193848 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 25, 25, 11, 17, 48, 48, 25, 25, 9, 9, 9, 5, 3, 3, 3, 3, 25, 25, 48, 48, 48, 25, 25] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/380 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193848 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 12, 22, 50, 50, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 50, 50, 50, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193848 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 Building ZINC000339193848 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193848 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 379) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193848 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 25, 25, 11, 17, 48, 48, 25, 25, 9, 9, 9, 5, 3, 3, 3, 3, 25, 25, 48, 48, 48, 25, 25] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 380) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193848 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 12, 22, 50, 50, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 50, 50, 50, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193848 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193848 Building ZINC000339193849 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193849 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/381 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193849 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 10, 13, 48, 48, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 48, 48, 48, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/382 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193849 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 9, 25, 25, 12, 23, 50, 50, 25, 25, 9, 9, 9, 5, 3, 3, 3, 3, 25, 25, 50, 50, 50, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193849 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 Building ZINC000339193849 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193849 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 381) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193849 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 10, 13, 48, 48, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 48, 48, 48, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 382) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193849 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 9, 25, 25, 12, 23, 50, 50, 25, 25, 9, 9, 9, 5, 3, 3, 3, 3, 25, 25, 50, 50, 50, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193849 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193849 Building ZINC000339193850 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193850 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/383 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193850 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 26, 26, 12, 17, 50, 50, 26, 26, 9, 9, 9, 5, 3, 3, 3, 3, 26, 26, 50, 50, 49, 26, 26] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/384 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193850 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 13, 16, 50, 50, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 50, 48, 49, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193850 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 Building ZINC000339193850 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193850 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 383) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193850 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 26, 26, 12, 17, 50, 50, 26, 26, 9, 9, 9, 5, 3, 3, 3, 3, 26, 26, 50, 50, 49, 26, 26] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 384) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1) `ZINC000339193850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193850 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 13, 16, 50, 50, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 50, 48, 49, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193850 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193850 Building ZINC000339193851 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193851 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/385 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193851 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 10, 13, 47, 47, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 48, 47, 47, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/386 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193851 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 9, 25, 25, 11, 22, 50, 50, 25, 25, 9, 9, 9, 5, 3, 3, 3, 3, 25, 25, 50, 50, 50, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193851 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 Building ZINC000339193851 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339193851 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 385) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339193851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193851 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 22, 22, 10, 13, 47, 47, 22, 22, 9, 9, 9, 5, 3, 3, 3, 3, 22, 22, 48, 47, 47, 22, 22] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 386) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1) `ZINC000339193851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339193851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000339193851 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc([S@](C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'C.3', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 5, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 9, 25, 25, 11, 22, 50, 50, 25, 25, 9, 9, 9, 5, 3, 3, 3, 3, 25, 25, 50, 50, 50, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339193851 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339193851 Building ZINC000339204694 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339204694 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/387 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1) `ZINC000339204694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339204694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339204694 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 12, 8, 1, 1, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 3, 21, 21, 21, 21, 10, 10, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 3, 10, 10, 21, 10, 10, 9] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/388 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1) `ZINC000339204694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339204694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339204694 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 12, 8, 1, 1, 1, 8, 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, 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] 0 hydrogens 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, 4, 10, 10, 7, 10, 22, 22, 22, 22, 10, 10, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 10, 10, 22, 10, 10, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339204694 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 Building ZINC000339204694 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339204694 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 387) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1) `ZINC000339204694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339204694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339204694 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 12, 8, 1, 1, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 3, 21, 21, 21, 21, 10, 10, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 3, 10, 10, 21, 10, 10, 9] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 388) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1) `ZINC000339204694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339204694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339204694 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(c3ncon3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 12, 8, 1, 1, 1, 8, 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, 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] 0 hydrogens 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, 4, 10, 10, 7, 10, 22, 22, 22, 22, 10, 10, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 4, 10, 10, 22, 10, 10, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339204694 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339204694 Building ZINC000339206962 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339206962 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/389 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/389' -> `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)cc1) `ZINC000339206962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339206962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339206962 none O=C(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 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] 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, 7, 7, 7] 0 hydrogens need rotated 50 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, 26, 29, 29, 24, 26, 50, 50, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 16, 16, 26, 26, 29, 50, 50, 50, 50, 50, 29, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/390 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/390' -> `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)cc1) `ZINC000339206962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339206962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339206962 none O=C(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 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] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 24, 28, 28, 22, 25, 50, 50, 28, 28, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 15, 24, 24, 28, 50, 50, 50, 50, 50, 28, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339206962 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 Building ZINC000339206962 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339206962 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 389) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000339206962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339206962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339206962 none O=C(NCCc1cnc(C2CC2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 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] 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, 7, 7, 7] 0 hydrogens need rotated 50 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, 26, 29, 29, 24, 26, 50, 50, 29, 29, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 16, 16, 26, 26, 29, 50, 50, 50, 50, 50, 29, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 390) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000339206962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339206962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339206962 none O=C(NCCc1cnc(C2CC2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 5, 5, 5, 8, 1, 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] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 24, 28, 28, 22, 25, 50, 50, 28, 28, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 15, 24, 24, 28, 50, 50, 50, 50, 50, 28, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339206962 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339206962 Building ZINC000566564732 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564732 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/391 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/392 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/393 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/393' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/394 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/394' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564732 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 Building ZINC000566564732 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564732 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 391) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 392) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 393) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 394) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564732 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 Building ZINC000566564732 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564732 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 391) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 392) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 393) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 394) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564732 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 Building ZINC000566564732 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564732 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 391) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 392) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 39, 50, 50, 39, 50, 50, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 17, 17, 17, 39, 39, 50, 50, 39, 50, 50, 17, 17] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 393) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 394) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564732.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564732 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 38, 50, 50, 38, 50, 50, 15, 15, 15, 15, 4, 3, 3, 3, 3, 15, 15, 15, 15, 38, 38, 50, 50, 38, 50, 50, 15, 15] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564732 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564732 Building ZINC000566564733 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564733 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/395 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/396 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/397 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/397' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/398 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/398' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564733 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 Building ZINC000566564733 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564733 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 395) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 396) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 397) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 398) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564733 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 Building ZINC000566564733 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564733 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 395) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 396) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 397) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 398) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564733 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 Building ZINC000566564733 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000566564733 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 395) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 396) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 12, 35, 50, 50, 35, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3, 12, 12, 12, 12, 35, 35, 50, 50, 35, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 397) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 398) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1) `ZINC000566564733.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000566564733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000566564733 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN(Cc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 34, 50, 50, 34, 50, 50, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14, 14, 14, 14, 34, 34, 50, 50, 34, 50, 50, 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, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000566564733 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000566564733 Building ZINC000182754738 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182754738 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/399 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000182754738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182754738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000182754738 none COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 14, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/400 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000182754738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182754738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000182754738 none COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 14, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182754738 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 Building ZINC000182754738 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182754738 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 399) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000182754738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182754738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000182754738 none COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 14, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 400) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2) `ZINC000182754738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182754738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000182754738 none COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)C2 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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 14, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000182754738 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000182754738 Building ZINC000339308572 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339308572 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/401 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1) `ZINC000339308572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339308572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339308572 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 2, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 16, 16, 16, 16, 16, 16, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/402 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1) `ZINC000339308572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339308572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339308572 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 24, 12, 12, 1, 1, 1, 2, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 16, 16, 16, 16, 16, 16, 12] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339308572 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 Building ZINC000339308572 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339308572 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 401) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1) `ZINC000339308572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339308572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339308572 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 2, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 16, 16, 16, 16, 16, 16, 10] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 402) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1) `ZINC000339308572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339308572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339308572 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCc3cc(F)c(F)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 15, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 24, 12, 12, 1, 1, 1, 2, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 16, 16, 16, 16, 16, 16, 12] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339308572 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339308572 Building ZINC000339527740 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339527740 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/403 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1) `ZINC000339527740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339527740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000339527740 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/404 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1) `ZINC000339527740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339527740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000339527740 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339527740 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 Building ZINC000339527740 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339527740 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 403) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1) `ZINC000339527740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339527740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000339527740 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 404) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1) `ZINC000339527740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339527740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000339527740 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2Cc3ccccc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 29, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339527740 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339527740 Building ZINC000339571850 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339571850 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/405 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CSCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339571850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339571850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339571850 none CC(C)CSCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.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, 5, 5, 5, 14, 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: [33, 33, 33, 25, 15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 15, 11, 11, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/406 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CSCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339571850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339571850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339571850 none CC(C)CSCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.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, 5, 5, 5, 14, 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, 38, 38, 30, 16, 12, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 12, 12, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339571850 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 Building ZINC000339571850 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339571850 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 405) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CSCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339571850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339571850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339571850 none CC(C)CSCCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.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, 5, 5, 5, 14, 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: [33, 33, 33, 25, 15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 15, 11, 11, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 406) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CSCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000339571850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339571850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339571850 none CC(C)CSCCCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.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, 5, 5, 5, 14, 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, 38, 38, 30, 16, 12, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 16, 16, 12, 12, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339571850 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339571850 Building ZINC000339581688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339581688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/407 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1) `ZINC000339581688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339581688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581688 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 19, 45, 45, 45, 45, 45, 12, 12, 12, 6, 6, 6, 6, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/408 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1) `ZINC000339581688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339581688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581688 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 43, 43, 43, 43, 43, 13, 13, 13, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43] 48 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339581688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 Building ZINC000339581688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339581688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 407) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1) `ZINC000339581688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339581688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581688 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 19, 45, 45, 45, 45, 45, 12, 12, 12, 6, 6, 6, 6, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 408) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1) `ZINC000339581688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339581688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581688 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 43, 43, 43, 43, 43, 13, 13, 13, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43] 48 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339581688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581688 Building ZINC000339581689 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339581689 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/409 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1) `ZINC000339581689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339581689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581689 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 44, 44, 44, 44, 44, 13, 13, 13, 6, 6, 6, 6, 44, 44, 44, 44, 44, 44] 48 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/410 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1) `ZINC000339581689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339581689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581689 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 46, 46, 46, 46, 46, 12, 12, 12, 6, 6, 6, 6, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339581689 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 Building ZINC000339581689 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339581689 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 409) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1) `ZINC000339581689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339581689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581689 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 44, 44, 44, 44, 44, 13, 13, 13, 6, 6, 6, 6, 44, 44, 44, 44, 44, 44] 48 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 410) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1) `ZINC000339581689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339581689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000339581689 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)[C@H]1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 1, 4, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 46, 46, 46, 46, 46, 12, 12, 12, 6, 6, 6, 6, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339581689 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339581689 Building ZINC000339645808 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339645808 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/411 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000339645808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339645808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339645808 none COCCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 41, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 42, 42, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/412 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000339645808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339645808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339645808 none COCCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 42, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 42, 42, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339645808 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 Building ZINC000339645808 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339645808 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 411) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000339645808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339645808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339645808 none COCCOc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 41, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 42, 42, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 412) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000339645808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339645808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339645808 none COCCOc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 42, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 42, 42, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 19] 50 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339645808 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339645808 Building ZINC000339652374 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339652374 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/413 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000339652374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339652374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000339652374 none CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 11, 18, 18, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 18, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/414 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000339652374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339652374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000339652374 none CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 11, 18, 18, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 18, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339652374 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 Building ZINC000339652374 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339652374 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 413) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000339652374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339652374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000339652374 none CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 11, 18, 18, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 18, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 414) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000339652374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339652374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000339652374 none CN(CC(=O)Nc1cccc(F)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 11, 18, 18, 18, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 18, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339652374 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339652374 Building ZINC000339717364 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339717364 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/415 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1) `ZINC000339717364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339717364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339717364 none Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 21, 17, 14, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 35, 35, 35, 35, 35, 21, 21, 17, 17, 17, 17, 13, 13, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/416 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1) `ZINC000339717364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339717364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339717364 none Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 20, 16, 14, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 34, 34, 34, 34, 34, 20, 20, 16, 16, 16, 16, 12, 12, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339717364 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 Building ZINC000339717364 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339717364 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 415) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1) `ZINC000339717364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339717364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339717364 none Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 21, 17, 14, 13, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 35, 35, 35, 35, 35, 21, 21, 17, 17, 17, 17, 13, 13, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 416) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1) `ZINC000339717364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339717364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339717364 none Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 20, 16, 14, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 34, 34, 34, 34, 34, 20, 20, 16, 16, 16, 16, 12, 12, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339717364 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339717364 Building ZINC000339764288 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339764288 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/417 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN(CCO)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000339764288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339764288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339764288 none CCCCCN(CCO)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 18, 14, 6, 2, 6, 15, 18, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 34, 35, 35, 35, 35, 27, 27, 19, 19, 14, 14, 15, 15, 18, 18, 54, 2, 2, 2, 2] 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]) total number of confs: 319 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/418 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN(CCO)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000339764288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339764288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339764288 none CCCCCN(CCO)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 26, 18, 14, 6, 2, 6, 14, 17, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 34, 35, 35, 35, 35, 28, 28, 19, 19, 14, 14, 14, 14, 17, 17, 51, 2, 2, 2, 2] 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]) total number of confs: 310 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339764288 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 Building ZINC000339764288 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339764288 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 417) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCCCN(CCO)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000339764288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339764288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339764288 none CCCCCN(CCO)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 18, 14, 6, 2, 6, 15, 18, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 34, 35, 35, 35, 35, 27, 27, 19, 19, 14, 14, 15, 15, 18, 18, 54, 2, 2, 2, 2] 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]) total number of confs: 319 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 418) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCCCN(CCO)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000339764288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339764288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000339764288 none CCCCCN(CCO)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 5, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 26, 18, 14, 6, 2, 6, 14, 17, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 34, 35, 35, 35, 35, 28, 28, 19, 19, 14, 14, 14, 14, 17, 17, 51, 2, 2, 2, 2] 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]) total number of confs: 310 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339764288 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339764288 Building ZINC000190435501 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190435501 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/419 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000190435501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190435501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000190435501 none CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 26, 26, 26, 17, 13, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 50, 50, 50, 50, 50, 45, 45, 26, 26, 17, 16, 15, 15, 12, 12, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1] 50 rigid atoms, others: [48, 49, 43, 44, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/420 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000190435501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190435501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000190435501 none CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 25, 25, 25, 25, 17, 13, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 50, 50, 50, 50, 50, 43, 43, 25, 25, 16, 17, 15, 15, 12, 12, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1] 50 rigid atoms, others: [48, 49, 43, 44, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190435501 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 Building ZINC000190435501 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190435501 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 419) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000190435501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190435501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000190435501 none CCCn1ccnc1CCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 26, 26, 26, 17, 13, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 50, 50, 50, 50, 50, 45, 45, 26, 26, 17, 16, 15, 15, 12, 12, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1] 50 rigid atoms, others: [48, 49, 43, 44, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 420) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1) `ZINC000190435501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190435501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000190435501 none CCCn1ccnc1CCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 25, 25, 25, 25, 17, 13, 12, 5, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 50, 50, 50, 50, 50, 43, 43, 25, 25, 16, 17, 15, 15, 12, 12, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1] 50 rigid atoms, others: [48, 49, 43, 44, 13, 15, 16, 17, 18, 19, 20, 21, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190435501 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190435501 Building ZINC000339842634 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339842634 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/421 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000339842634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339842634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339842634 none O=C(N[C@@H](CCO)C1CCCCC1)[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', '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, 7, 5, 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: [4, 1, 4, 4, 9, 9, 16, 19, 11, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 19, 19, 57, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/422 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000339842634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339842634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339842634 none O=C(N[C@@H](CCO)C1CCCCC1)[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', '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, 7, 5, 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: [3, 1, 3, 3, 8, 8, 12, 16, 11, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 16, 16, 48, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339842634 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 Building ZINC000339842634 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339842634 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 421) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000339842634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339842634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339842634 none O=C(N[C@@H](CCO)C1CCCCC1)[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', '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, 7, 5, 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: [4, 1, 4, 4, 9, 9, 16, 19, 11, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 19, 19, 57, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 422) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000339842634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339842634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000339842634 none O=C(N[C@@H](CCO)C1CCCCC1)[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', '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, 7, 5, 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: [3, 1, 3, 3, 8, 8, 12, 16, 11, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 16, 16, 48, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339842634 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339842634 Building ZINC000339874144 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339874144 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/423 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/423' -> `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(C(F)(F)F)CC2)cn1) `ZINC000339874144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339874144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339874144 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC=C(C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 10, 16, 16, 10, 10, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 13, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/424 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/424' -> `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(C(F)(F)F)CC2)cn1) `ZINC000339874144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339874144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339874144 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC=C(C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 8, 8, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339874144 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 Building ZINC000339874144 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339874144 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 423) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC=C(C(F)(F)F)CC2)cn1) `ZINC000339874144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339874144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339874144 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC=C(C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 10, 16, 16, 10, 10, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 13, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 424) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC=C(C(F)(F)F)CC2)cn1) `ZINC000339874144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339874144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000339874144 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC=C(C(F)(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 15, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 15, 8, 8, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339874144 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339874144 Building ZINC000339871144 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339871144 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/425 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339871144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871144 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 7, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/426 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339871144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871144 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens 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, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 6, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339871144 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 Building ZINC000339871144 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339871144 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 425) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339871144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871144 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 7, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 426) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339871144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871144 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens 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, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 6, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339871144 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871144 Building ZINC000339871145 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339871145 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/427 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339871145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871145 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens 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, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/428 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339871145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871145 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens 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, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 6, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339871145 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 Building ZINC000339871145 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000339871145 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 427) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000339871145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871145 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens 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, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 428) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C) `ZINC000339871145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000339871145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000339871145 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1c(C)noc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 8, 12, 1, 5, 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, 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] 0 hydrogens 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, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 6, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000339871145 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000339871145 Building ZINC000183549169 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183549169 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/429 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1) `ZINC000183549169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183549169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000183549169 none Cn1cnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 24, 24, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 31, 31, 31, 31, 31, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/430 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1) `ZINC000183549169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183549169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000183549169 none Cn1cnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 24, 24, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 31, 31, 31, 31, 31, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183549169 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 Building ZINC000183549169 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183549169 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 429) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1) `ZINC000183549169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183549169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000183549169 none Cn1cnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 24, 24, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 31, 31, 31, 31, 31, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 430) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1) `ZINC000183549169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183549169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000183549169 none Cn1cnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 24, 24, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 31, 31, 31, 31, 31, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183549169 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183549169 Building ZINC000183540524 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183540524 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/431 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1) `ZINC000183540524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183540524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183540524 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 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, 3, 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: [8, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 41, 41, 41, 41, 28, 28, 8, 8, 8, 7, 7, 7, 7, 6, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/432 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1) `ZINC000183540524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183540524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183540524 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 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, 3, 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: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 41, 41, 41, 41, 28, 28, 8, 8, 8, 7, 7, 7, 7, 7, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183540524 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 Building ZINC000183540524 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183540524 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 431) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1) `ZINC000183540524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183540524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183540524 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 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, 3, 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: [8, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 41, 41, 41, 41, 28, 28, 8, 8, 8, 7, 7, 7, 7, 6, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 432) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1) `ZINC000183540524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183540524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183540524 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 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, 3, 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: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 41, 41, 41, 41, 28, 28, 8, 8, 8, 7, 7, 7, 7, 7, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 28] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183540524 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183540524 Building ZINC000183599456 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183599456 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/433 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183599456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599456 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 3, 6, 6, 1, 1, 1, 2, 8, 12, 25, 25, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 25, 7, 7, 7, 6, 6, 6, 6, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/434 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183599456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599456 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 9, 14, 25, 25, 25, 25, 25, 25, 25, 25, 39, 39, 29, 39, 39, 25, 6, 6, 6, 5, 5, 5, 5, 25, 25, 25, 25, 25, 39, 39, 39, 39, 39, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183599456 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 Building ZINC000183599456 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183599456 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 433) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183599456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599456 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 3, 6, 6, 1, 1, 1, 2, 8, 12, 25, 25, 25, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 25, 7, 7, 7, 6, 6, 6, 6, 25, 25, 25, 25, 25, 36, 36, 36, 36, 36, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 434) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183599456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599456 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 9, 14, 25, 25, 25, 25, 25, 25, 25, 25, 39, 39, 29, 39, 39, 25, 6, 6, 6, 5, 5, 5, 5, 25, 25, 25, 25, 25, 39, 39, 39, 39, 39, 25, 25] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183599456 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599456 Building ZINC000183599472 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183599472 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/435 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183599472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599472 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 33, 33, 25, 33, 33, 25, 7, 7, 7, 6, 6, 6, 6, 25, 25, 25, 25, 25, 33, 33, 25, 33, 33, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/436 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183599472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599472 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 35, 35, 25, 35, 35, 25, 6, 6, 6, 5, 5, 5, 5, 25, 25, 25, 25, 25, 35, 35, 25, 35, 35, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183599472 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 Building ZINC000183599472 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183599472 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 435) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183599472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599472 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 33, 33, 25, 33, 33, 25, 7, 7, 7, 6, 6, 6, 6, 25, 25, 25, 25, 25, 33, 33, 25, 33, 33, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 436) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000183599472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183599472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599472 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 35, 35, 25, 35, 35, 25, 6, 6, 6, 5, 5, 5, 5, 25, 25, 25, 25, 25, 35, 35, 25, 35, 35, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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/25650/xaq-8058115.17/working/building/ZINC000183599472 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183599472 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599472 Building ZINC000183599488 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183599488 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/437 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000183599488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183599488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599488 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 26, 26, 26, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 26, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 26, 26] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/438 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000183599488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183599488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599488 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 8, 12, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 25, 32, 32, 24, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 32, 32, 24, 32, 32, 24, 24] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183599488 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 Building ZINC000183599488 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183599488 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 437) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000183599488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183599488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599488 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 14, 26, 26, 26, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 26, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 35, 35, 26, 35, 35, 26, 26] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 438) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000183599488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183599488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183599488 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)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', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 8, 12, 24, 24, 24, 24, 24, 24, 24, 24, 32, 32, 25, 32, 32, 24, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 32, 32, 24, 32, 32, 24, 24] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183599488 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183599488 Building ZINC000183694853 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183694853 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/439 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1) `ZINC000183694853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183694853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000183694853 none Cn1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 24, 24, 24, 24, 24, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/440 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1) `ZINC000183694853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183694853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000183694853 none Cn1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 24, 24, 24, 24, 24, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183694853 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 Building ZINC000183694853 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183694853 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 439) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1) `ZINC000183694853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183694853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000183694853 none Cn1cnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 24, 24, 24, 24, 24, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 440) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1) `ZINC000183694853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183694853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000183694853 none Cn1cnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 24, 24, 24, 24, 24, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183694853 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183694853 Building ZINC000183701424 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183701424 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/441 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C) `ZINC000183701424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183701424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000183701424 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/442 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C) `ZINC000183701424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183701424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000183701424 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183701424 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 Building ZINC000183701424 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183701424 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 441) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C) `ZINC000183701424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183701424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000183701424 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 442) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C) `ZINC000183701424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183701424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000183701424 none CN(C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183701424 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183701424 Building ZINC000340084191 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340084191 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/443 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cn1) `ZINC000340084191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340084191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000340084191 none Cn1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 34, 34, 34, 34, 34, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 13, 13, 4, 3, 3, 3, 3, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/444 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cn1) `ZINC000340084191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340084191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000340084191 none Cn1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 33, 33, 33, 33, 33, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 13, 13, 4, 3, 3, 3, 3, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340084191 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 Building ZINC000340084191 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340084191 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 443) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cn1) `ZINC000340084191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340084191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000340084191 none Cn1cc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 34, 34, 34, 34, 34, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 13, 13, 4, 3, 3, 3, 3, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 444) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cn1) `ZINC000340084191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340084191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000340084191 none Cn1cc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 33, 33, 33, 33, 33, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 13, 13, 4, 3, 3, 3, 3, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340084191 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340084191 Building ZINC000340085099 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340085099 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/445 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000340085099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340085099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000340085099 none COc1ccc(OC)c(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 50, 26, 19, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 49, 49, 50, 50, 50, 25, 26, 25, 25, 13, 13, 2, 2, 2, 2, 2, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/446 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000340085099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340085099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000340085099 none COc1ccc(OC)c(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 48, 48, 48, 48, 48, 50, 25, 19, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 49, 49, 49, 48, 48, 50, 50, 50, 24, 25, 24, 24, 12, 12, 2, 3, 3, 3, 3, 48] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340085099 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 Building ZINC000340085099 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340085099 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 445) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(OC)c(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000340085099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340085099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000340085099 none COc1ccc(OC)c(CCCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 50, 26, 19, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 49, 49, 50, 50, 50, 25, 26, 25, 25, 13, 13, 2, 2, 2, 2, 2, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 446) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(OC)c(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000340085099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340085099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000340085099 none COc1ccc(OC)c(CCCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 48, 48, 48, 48, 48, 50, 25, 19, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 49, 49, 49, 48, 48, 50, 50, 50, 24, 25, 24, 24, 12, 12, 2, 3, 3, 3, 3, 48] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340085099 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340085099 Building ZINC000340104094 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104094 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/447 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/448 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/449 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/449' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/450 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/450' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104094 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 Building ZINC000340104094 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104094 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 447) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 448) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 449) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 450) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104094 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 Building ZINC000340104094 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104094 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 447) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 448) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 449) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 450) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104094 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 Building ZINC000340104094 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104094 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 447) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 448) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 37, 37, 37, 46, 46, 42, 46, 46, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 46, 46, 42, 46, 46] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 449) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 450) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104094.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104094 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 43, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104094 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104094 Building ZINC000340097061 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097061 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/451 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097061 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 16, 16, 13, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 13, 13, 13, 13, 13, 13, 13, 13, 16, 16, 13, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/452 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097061 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 12, 15, 15, 8, 8, 16, 16, 16, 16, 16, 8, 4, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 12, 15, 15, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097061 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 Building ZINC000340097061 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097061 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 451) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097061 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 16, 16, 13, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 4, 13, 13, 13, 13, 13, 13, 13, 13, 16, 16, 13, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 452) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097061 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 12, 15, 15, 8, 8, 16, 16, 16, 16, 16, 8, 4, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 12, 15, 15, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097061 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097061 Building ZINC000340097063 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097063 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/453 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097063 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 12, 12, 1, 1, 1, 1, 5, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 12, 12, 25, 25, 25, 25, 25, 12, 5, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/454 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097063 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10, 10, 25, 25, 25, 25, 25, 10, 4, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097063 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 Building ZINC000340097063 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097063 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 453) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097063 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 12, 12, 1, 1, 1, 1, 5, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 12, 12, 25, 25, 25, 25, 25, 12, 5, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 12] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 454) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097063 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 10, 10, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10, 10, 25, 25, 25, 25, 25, 10, 4, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097063 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097063 Building ZINC000340097065 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097065 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/455 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097065 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 9, 14, 14, 8, 8, 21, 21, 21, 21, 21, 8, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/456 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097065 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 25, 25, 25, 25, 25, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097065 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 Building ZINC000340097065 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097065 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 455) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097065 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 9, 14, 14, 8, 8, 21, 21, 21, 21, 21, 8, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 456) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1) `ZINC000340097065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097065 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 25, 25, 25, 25, 25, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097065 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097065 Building ZINC000340097067 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097067 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/457 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097067 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 6, 6, 14, 14, 14, 14, 14, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 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, 45, 46]) total number of confs: 87 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/458 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097067 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 20, 20, 7, 7, 17, 17, 17, 17, 17, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 20, 20, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097067 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 Building ZINC000340097067 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340097067 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 457) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340097067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097067 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 6, 6, 14, 14, 14, 14, 14, 6, 4, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 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, 45, 46]) total number of confs: 87 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 458) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1) `ZINC000340097067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340097067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000340097067 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCC[C@@H]2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 20, 20, 7, 7, 17, 17, 17, 17, 17, 7, 4, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 20, 20, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340097067 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340097067 Building ZINC000340104096 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104096 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/459 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/460 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/461 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/461' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/462 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/462' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104096 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 Building ZINC000340104096 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104096 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 459) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 460) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 461) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 462) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104096 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 Building ZINC000340104096 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104096 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 459) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 460) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 461) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 462) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104096 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 Building ZINC000340104096 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104096 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 459) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 460) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 12, 47, 6, 1, 6, 1, 1, 1, 5, 5, 2, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 461) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 462) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1) `ZINC000340104096.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104096 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 44, 7, 1, 7, 1, 1, 1, 5, 5, 1, 1, 5, 5, 44, 44, 44, 48, 48, 48, 48, 48, 44, 44, 44, 44, 44, 44, 44, 7, 5, 5, 5, 5, 48, 48, 48, 48, 48] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104096 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104096 Building ZINC000340104102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/463 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/464 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/465 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/465' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/466 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/466' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 Building ZINC000340104102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 463) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 464) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 465) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 466) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 Building ZINC000340104102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 463) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 464) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 465) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 466) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 Building ZINC000340104102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 463) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 464) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 16, 47, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 47, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 47, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 465) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 466) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104102.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104102 none CN1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 48, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 48, 48, 48, 49, 49, 48, 49, 49, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 49, 49, 48, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104102 Building ZINC000340104107 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104107 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/467 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/468 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/469 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/469' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/470 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/470' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104107 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 Building ZINC000340104107 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104107 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 467) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 468) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 469) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 470) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104107 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 Building ZINC000340104107 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104107 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 467) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 468) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 469) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 470) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104107 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 Building ZINC000340104107 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340104107 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 467) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 468) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 37, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 37, 37, 37, 47, 47, 43, 47, 47, 37, 37, 37, 37, 37, 37, 37, 6, 5, 5, 5, 5, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 469) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 470) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1) `ZINC000340104107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340104107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340104107 none CN1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 34, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 34, 34, 46, 46, 38, 46, 46, 34, 34, 34, 34, 34, 34, 34, 6, 5, 5, 5, 5, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340104107 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340104107 Building ZINC000183809302 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183809302 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/471 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCN(CC)CC)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000183809302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183809302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000183809302 none CCCN(CCN(CC)CC)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 7, 7, 20, 21, 20, 21, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 8, 8, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/472 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCN(CC)CC)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000183809302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183809302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000183809302 none CCCN(CCN(CC)CC)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 8, 8, 20, 21, 20, 22, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 9, 9, 8, 8, 8, 8, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183809302 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 Building ZINC000183809302 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183809302 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 471) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCN(CC)CC)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000183809302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183809302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000183809302 none CCCN(CCN(CC)CC)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 7, 7, 20, 21, 20, 21, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 8, 8, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 472) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCN(CC)CC)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000183809302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183809302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000183809302 none CCCN(CCN(CC)CC)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 8, 8, 20, 21, 20, 22, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 9, 9, 8, 8, 8, 8, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000183809302 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000183809302 Building ZINC000340109830 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340109830 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/473 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340109830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109830 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 17, 10, 10, 10, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/474 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340109830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109830 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 18, 10, 10, 10, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340109830 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 Building ZINC000340109830 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340109830 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 473) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340109830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109830 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 17, 10, 10, 10, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 474) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340109830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109830 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 18, 10, 10, 10, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340109830 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109830 Building ZINC000340109832 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340109832 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/475 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340109832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109832 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 18, 10, 10, 10, 4, 4, 11, 11, 11, 11, 11, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/476 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340109832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109832 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 18, 11, 11, 11, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 11, 11, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340109832 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 Building ZINC000340109832 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340109832 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 475) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340109832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109832 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 18, 10, 10, 10, 4, 4, 11, 11, 11, 11, 11, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 476) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1) `ZINC000340109832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340109832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000340109832 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCc3cc(OC)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 18, 11, 11, 11, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 11, 11, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340109832 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340109832 Building ZINC000567360182 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360182 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/477 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360182 none CCC[C@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 30, 14, 30, 30, 4, 14, 14, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 41, 41, 41, 41, 41, 40, 40, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 361 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/478 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360182 none CCC[C@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 41, 30, 15, 30, 29, 4, 15, 15, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 43, 43, 41, 41, 30, 30, 30, 27, 27, 81, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 336 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360182 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 Building ZINC000567360182 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360182 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 477) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360182 none CCC[C@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 30, 14, 30, 30, 4, 14, 14, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 41, 41, 41, 41, 41, 40, 40, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 361 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 478) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360182 none CCC[C@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 41, 30, 15, 30, 29, 4, 15, 15, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 43, 43, 41, 41, 30, 30, 30, 27, 27, 81, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 336 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360182 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360182 Building ZINC000567360183 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360183 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/479 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360183 none CCC[C@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 31, 16, 33, 31, 4, 16, 16, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 33, 33, 33, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/480 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360183 none CCC[C@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 30, 15, 31, 29, 4, 15, 15, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 31, 31, 31, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360183 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 Building ZINC000567360183 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360183 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 479) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360183 none CCC[C@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 31, 16, 33, 31, 4, 16, 16, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 33, 33, 33, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 480) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360183 none CCC[C@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 30, 15, 31, 29, 4, 15, 15, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 31, 31, 31, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360183 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360183 Building ZINC000567360184 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360184 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/481 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360184 none CCC[C@@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 32, 15, 33, 31, 4, 15, 15, 34, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 33, 33, 33, 34, 34, 102, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/482 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360184 none CCC[C@@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 31, 16, 32, 30, 4, 16, 16, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37, 32, 32, 32, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360184 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 Building ZINC000567360184 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360184 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 481) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360184 none CCC[C@@H](C)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 32, 15, 33, 31, 4, 15, 15, 34, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 33, 33, 33, 34, 34, 102, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 482) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360184 none CCC[C@@H](C)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 31, 16, 32, 30, 4, 16, 16, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37, 32, 32, 32, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360184 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360184 Building ZINC000567360185 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360185 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/483 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360185 none CCC[C@@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 41, 30, 15, 30, 29, 4, 15, 15, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 43, 43, 41, 41, 30, 30, 30, 27, 27, 81, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 333 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/484 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360185 none CCC[C@@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 30, 14, 30, 30, 4, 14, 14, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 41, 41, 41, 41, 41, 40, 40, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 357 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360185 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 Building ZINC000567360185 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567360185 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 483) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567360185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360185 none CCC[C@@H](C)[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 41, 30, 15, 30, 29, 4, 15, 15, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 43, 43, 41, 41, 30, 30, 30, 27, 27, 81, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 333 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 484) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000567360185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567360185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000567360185 none CCC[C@@H](C)[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.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, 5, 5, 7, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 40, 30, 14, 30, 30, 4, 14, 14, 33, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 41, 41, 41, 41, 41, 40, 40, 30, 30, 30, 33, 33, 99, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 357 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567360185 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567360185 Building ZINC000340148897 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148897 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/485 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148897 none C[C@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 11, 25, 25, 27, 27, 11, 11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 25, 25, 25, 27, 27, 27, 27, 27, 11, 11, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/486 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148897 none C[C@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 12, 12, 12, 12, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 27, 27, 27, 28, 28, 28, 28, 28, 12, 12, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340148897 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 Building ZINC000340148897 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148897 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 485) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148897 none C[C@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 11, 25, 25, 27, 27, 11, 11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 25, 25, 25, 27, 27, 27, 27, 27, 11, 11, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 486) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148897 none C[C@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 12, 12, 12, 12, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 27, 27, 27, 28, 28, 28, 28, 28, 12, 12, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340148897 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148897 Building ZINC000340148898 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148898 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/487 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148898 none C[C@@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 29, 29, 29, 29, 13, 13, 13, 13, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/488 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148898 none C[C@@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 22, 22, 23, 23, 12, 12, 12, 12, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 22, 22, 22, 23, 23, 23, 23, 23, 12, 12, 5, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340148898 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 Building ZINC000340148898 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148898 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 487) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148898 none C[C@@H](C1CC1)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 13, 29, 29, 29, 29, 13, 13, 13, 13, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 488) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340148898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340148898 none C[C@@H](C1CC1)n1nccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 22, 22, 23, 23, 12, 12, 12, 12, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 22, 22, 22, 23, 23, 23, 23, 23, 12, 12, 5, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340148898 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340148898 Building ZINC000340149857 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340149857 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/489 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)cc(C)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340149857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340149857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340149857 none COc1nc(C)cc(C)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 22, 22, 22, 22, 22, 22, 22, 22, 13, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 13, 13, 5, 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]) total number of confs: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/490 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)cc(C)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340149857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340149857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340149857 none COc1nc(C)cc(C)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 13, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 22, 22, 22, 22, 22, 22, 22, 13, 13, 5, 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]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340149857 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 Building ZINC000340149857 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340149857 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 489) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)cc(C)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340149857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340149857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340149857 none COc1nc(C)cc(C)c1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 22, 22, 22, 22, 22, 22, 22, 22, 13, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 13, 13, 5, 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]) total number of confs: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 490) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C)cc(C)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340149857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340149857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340149857 none COc1nc(C)cc(C)c1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 13, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 22, 22, 22, 22, 22, 22, 22, 13, 13, 5, 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]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340149857 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340149857 Building ZINC000340165587 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340165587 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/491 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340165587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340165587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000340165587 none CN(CCCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 8, 12, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 12, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 12, 13, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/492 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340165587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340165587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000340165587 none CN(CCCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 8, 12, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 11, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 12, 13, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340165587 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 Building ZINC000340165587 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340165587 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 491) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340165587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340165587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000340165587 none CN(CCCC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 8, 12, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 12, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 12, 13, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 492) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340165587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340165587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000340165587 none CN(CCCC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 8, 12, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 11, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 12, 13, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340165587 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340165587 Building ZINC000340176975 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340176975 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/493 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340176975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176975 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 13, 14, 14, 14, 14, 14, 14, 10, 15, 15, 4, 4, 14, 14, 14, 14, 14, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/494 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340176975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176975 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 13, 14, 14, 13, 14, 14, 14, 8, 13, 13, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 13, 13, 13, 13, 13, 13, 13, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340176975 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 Building ZINC000340176975 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340176975 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 493) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340176975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176975 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 13, 14, 14, 14, 14, 14, 14, 10, 15, 15, 4, 4, 14, 14, 14, 14, 14, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 494) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340176975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176975 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 13, 14, 14, 13, 14, 14, 14, 8, 13, 13, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 13, 13, 13, 13, 13, 13, 13, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340176975 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176975 Building ZINC000340176977 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340176977 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/495 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340176977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176977 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 9, 9, 14, 15, 15, 14, 14, 15, 15, 9, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/496 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340176977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176977 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 13, 14, 14, 13, 14, 14, 14, 10, 14, 14, 4, 4, 16, 16, 16, 16, 16, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340176977 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 Building ZINC000340176977 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340176977 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 495) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340176977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176977 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 9, 9, 14, 15, 15, 14, 14, 15, 15, 9, 14, 14, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 496) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1) `ZINC000340176977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340176977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340176977 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](Cc2ccc(F)cc2)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 10, 13, 14, 14, 13, 14, 14, 14, 10, 14, 14, 4, 4, 16, 16, 16, 16, 16, 4, 4, 4, 4, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340176977 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340176977 Building ZINC000340233249 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340233249 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/497 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340233249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340233249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340233249 none O=C(N(CCCO)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 11, 17, 4, 8, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 17, 16, 51, 8, 8, 9, 9, 9, 9, 9, 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]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/498 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340233249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340233249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340233249 none O=C(N(CCCO)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 11, 17, 4, 8, 9, 9, 8, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 16, 17, 51, 8, 8, 9, 9, 9, 9, 9, 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]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340233249 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 Building ZINC000340233249 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340233249 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 497) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340233249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340233249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340233249 none O=C(N(CCCO)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 11, 17, 4, 8, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 17, 16, 51, 8, 8, 9, 9, 9, 9, 9, 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]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 498) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCO)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340233249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340233249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340233249 none O=C(N(CCCO)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 11, 17, 4, 8, 9, 9, 8, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 16, 17, 51, 8, 8, 9, 9, 9, 9, 9, 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]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340233249 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340233249 Building ZINC000340277790 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277790 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/499 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277790 none CC[C@@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 4, 12, 12, 25, 34, 34, 34, 45, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 25, 25, 34, 34, 34, 45, 45, 135, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 430 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/500 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277790 none CC[C@@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 4, 15, 15, 26, 34, 34, 34, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 25, 26, 26, 34, 34, 34, 42, 42, 126, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 412 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277790 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 Building ZINC000340277790 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277790 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 499) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277790 none CC[C@@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 4, 12, 12, 25, 34, 34, 34, 45, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 25, 25, 34, 34, 34, 45, 45, 135, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 430 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 500) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277790 none CC[C@@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 4, 15, 15, 26, 34, 34, 34, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 25, 26, 26, 34, 34, 34, 42, 42, 126, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 412 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277790 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277790 Building ZINC000340277791 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277791 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/501 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277791 none CC[C@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 4, 13, 13, 26, 32, 32, 32, 43, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 26, 26, 32, 32, 32, 43, 43, 129, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 397 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/502 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277791 none CC[C@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 12, 4, 12, 12, 24, 29, 29, 29, 45, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 18, 18, 18, 18, 18, 24, 24, 29, 29, 29, 45, 45, 135, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 394 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277791 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 Building ZINC000340277791 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277791 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 501) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277791 none CC[C@H](C[C@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 4, 13, 13, 26, 32, 32, 32, 43, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 26, 26, 32, 32, 32, 43, 43, 129, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 397 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 502) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277791 none CC[C@H](C[C@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 12, 4, 12, 12, 24, 29, 29, 29, 45, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 18, 18, 18, 18, 18, 24, 24, 29, 29, 29, 45, 45, 135, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 394 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277791 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277791 Building ZINC000340277793 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277793 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/503 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277793 none CC[C@@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 4, 13, 13, 25, 30, 30, 30, 45, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 19, 19, 19, 25, 25, 30, 30, 30, 45, 45, 135, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 397 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/504 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277793 none CC[C@@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 4, 13, 13, 25, 31, 31, 31, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 25, 25, 31, 31, 31, 42, 42, 126, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277793 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 Building ZINC000340277793 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277793 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 503) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277793 none CC[C@@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 4, 13, 13, 25, 30, 30, 30, 45, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 19, 19, 19, 25, 25, 30, 30, 30, 45, 45, 135, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 397 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 504) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277793 none CC[C@@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 4, 13, 13, 25, 31, 31, 31, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 25, 25, 31, 31, 31, 42, 42, 126, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277793 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277793 Building ZINC000340277796 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277796 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/505 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277796 none CC[C@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 4, 15, 15, 25, 33, 33, 33, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 33, 33, 33, 42, 42, 126, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/506 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277796 none CC[C@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 4, 12, 12, 24, 33, 33, 33, 43, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 24, 24, 33, 33, 33, 43, 43, 129, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277796 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 Building ZINC000340277796 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340277796 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 505) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340277796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277796 none CC[C@H](C[C@@H](C)CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 4, 15, 15, 25, 33, 33, 33, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 33, 33, 33, 42, 42, 126, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 506) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000340277796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340277796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000340277796 none CC[C@H](C[C@@H](C)CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 7, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 4, 12, 12, 24, 33, 33, 33, 43, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 24, 24, 33, 33, 33, 43, 43, 129, 4, 3, 3, 3, 3] 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340277796 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340277796 Building ZINC000184050620 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184050620 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/507 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1) `ZINC000184050620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050620 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 23, 23, 23, 40, 44, 44, 40, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 23, 23, 23, 40, 40, 44, 44, 88, 44, 44] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/508 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1) `ZINC000184050620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050620 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 19, 19, 19, 39, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 19, 19, 19, 39, 39, 42, 42, 84, 42, 42] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184050620 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 Building ZINC000184050620 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184050620 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 507) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1) `ZINC000184050620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050620 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 23, 23, 23, 40, 44, 44, 40, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 23, 23, 23, 40, 40, 44, 44, 88, 44, 44] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 508) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1) `ZINC000184050620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184050620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050620 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 19, 19, 19, 39, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 19, 19, 19, 39, 39, 42, 42, 84, 42, 42] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184050620 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050620 Building ZINC000184050644 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184050644 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/509 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1) `ZINC000184050644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184050644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050644 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 20, 20, 20, 40, 43, 43, 40, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 20, 20, 20, 40, 40, 43, 43, 86, 43, 43] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 289 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/510 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1) `ZINC000184050644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184050644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050644 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 23, 23, 23, 40, 44, 44, 40, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 23, 23, 23, 40, 40, 44, 44, 88, 44, 44] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184050644 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 Building ZINC000184050644 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184050644 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 509) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1) `ZINC000184050644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184050644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050644 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 20, 20, 20, 40, 43, 43, 40, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 20, 20, 20, 40, 40, 43, 43, 86, 43, 43] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 289 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 510) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1) `ZINC000184050644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184050644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184050644 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)Cc1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 23, 23, 23, 40, 44, 44, 40, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 23, 23, 23, 40, 40, 44, 44, 88, 44, 44] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 294 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000184050644 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000184050644 Building ZINC000567480957 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567480957 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/511 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000567480957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567480957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000567480957 none O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7] 1 hydrogens 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, 5, 12, 12, 12, 12, 12, 12, 30, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 12, 12, 12, 12, 30, 50, 50, 50, 50, 12, 12, 12, 12, 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, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/512 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000567480957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567480957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000567480957 none O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 14, 14, 14, 14, 14, 14, 32, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 14, 14, 14, 14, 32, 50, 50, 50, 50, 14, 14, 14, 14, 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, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567480957 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 Building ZINC000567480957 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000567480957 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 511) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000567480957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000567480957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000567480957 none O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7] 1 hydrogens 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, 5, 12, 12, 12, 12, 12, 12, 30, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 12, 12, 12, 12, 30, 50, 50, 50, 50, 12, 12, 12, 12, 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, 42, 43, 44, 45]) total number of confs: 141 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 512) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000567480957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000567480957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000567480957 none O=C(N[C@H]1CC[C@H](Nc2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 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, 7, 7, 4, 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, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 14, 14, 14, 14, 14, 14, 32, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 14, 14, 14, 14, 32, 50, 50, 50, 50, 14, 14, 14, 14, 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, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000567480957 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000567480957 Building ZINC000340332896 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340332896 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/513 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000340332896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340332896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000340332896 none Cc1cc(CN(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 23, 24, 24, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 8, 8, 8, 8, 8, 23, 23, 24, 24, 24, 24, 24, 24, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/514 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000340332896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340332896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000340332896 none Cc1cc(CN(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 21, 22, 22, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 8, 8, 8, 8, 8, 21, 21, 22, 22, 22, 22, 22, 22, 8, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340332896 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 Building ZINC000340332896 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340332896 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 513) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(CN(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000340332896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340332896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000340332896 none Cc1cc(CN(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 23, 24, 24, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 8, 8, 8, 8, 8, 23, 23, 24, 24, 24, 24, 24, 24, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 514) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(CN(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000340332896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340332896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000340332896 none Cc1cc(CN(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 21, 22, 22, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 8, 8, 8, 8, 8, 21, 21, 22, 22, 22, 22, 22, 22, 8, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340332896 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340332896 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340332896 Building ZINC000340390254 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340390254 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/515 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340390254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390254 none O=C(N[C@@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 7, 12, 12, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 20, 20, 20, 20, 12, 12, 12, 12, 12, 7, 8, 8, 7, 8, 8, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/516 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340390254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390254 none O=C(N[C@@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 23, 23, 23, 23, 13, 13, 13, 13, 13, 7, 8, 8, 8, 8, 8, 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, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340390254 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 Building ZINC000340390254 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340390254 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 515) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340390254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390254 none O=C(N[C@@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 7, 12, 12, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 20, 20, 20, 20, 12, 12, 12, 12, 12, 7, 8, 8, 7, 8, 8, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 516) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340390254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390254 none O=C(N[C@@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 23, 23, 23, 23, 23, 8, 13, 13, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 23, 23, 23, 23, 13, 13, 13, 13, 13, 7, 8, 8, 8, 8, 8, 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, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340390254 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390254 Building ZINC000340390256 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340390256 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/517 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340390256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390256 none O=C(N[C@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 29, 29, 29, 29, 29, 8, 12, 12, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 29, 29, 29, 29, 12, 12, 12, 12, 12, 7, 8, 8, 7, 8, 8, 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, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/518 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340390256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390256 none O=C(N[C@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 25, 25, 25, 25, 25, 8, 13, 13, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 25, 25, 25, 25, 13, 13, 13, 13, 13, 7, 8, 8, 8, 8, 8, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340390256 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 Building ZINC000340390256 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340390256 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 517) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340390256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390256 none O=C(N[C@H](c1cccnc1)C1CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 29, 29, 29, 29, 29, 8, 12, 12, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 29, 29, 29, 29, 12, 12, 12, 12, 12, 7, 8, 8, 7, 8, 8, 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, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 518) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000340390256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340390256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340390256 none O=C(N[C@H](c1cccnc1)C1CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 25, 25, 25, 25, 25, 8, 13, 13, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 25, 25, 25, 25, 13, 13, 13, 13, 13, 7, 8, 8, 8, 8, 8, 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, 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/25650/xaq-8058115.17/working/building/ZINC000340390256 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340390256 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340390256 Building ZINC000340426541 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340426541 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/519 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000340426541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340426541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000340426541 none CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 24, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 10, 10, 10, 24, 24, 24, 10, 10, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/520 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000340426541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340426541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000340426541 none CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 25, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 10, 10, 25, 25, 25, 10, 10, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340426541 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 Building ZINC000340426541 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340426541 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 519) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000340426541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340426541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000340426541 none CC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 24, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 10, 10, 10, 24, 24, 24, 10, 10, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 520) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000340426541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340426541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000340426541 none CC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 10, 25, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 10, 10, 10, 25, 25, 25, 10, 10, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340426541 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340426541 Building ZINC000340455733 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340455733 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/521 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340455733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455733 none CCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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, 42, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 15, 48, 48, 48, 48, 48, 42, 42, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/522 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340455733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455733 none CCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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, 48, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 18, 18, 18, 49, 49, 49, 49, 49, 48, 48, 18, 18, 3, 3, 3, 3, 18, 18, 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, 34, 35, 36, 37]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340455733 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 Building ZINC000340455733 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340455733 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 521) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340455733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455733 none CCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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, 42, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 15, 48, 48, 48, 48, 48, 42, 42, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 522) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340455733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455733 none CCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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, 48, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 18, 18, 18, 49, 49, 49, 49, 49, 48, 48, 18, 18, 3, 3, 3, 3, 18, 18, 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, 34, 35, 36, 37]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340455733 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455733 Building ZINC000340455734 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340455734 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/523 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340455734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455734 none CCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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, 46, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 48, 48, 48, 48, 48, 46, 46, 17, 17, 3, 3, 3, 3, 17, 17, 17, 17] 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: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/524 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340455734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455734 none CCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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: [47, 43, 18, 18, 18, 18, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 47, 47, 47, 47, 47, 43, 43, 18, 18, 3, 3, 3, 3, 18, 18, 18, 18] 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: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340455734 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 Building ZINC000340455734 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340455734 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 523) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340455734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455734 none CCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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, 46, 17, 17, 17, 17, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 48, 48, 48, 48, 48, 46, 46, 17, 17, 3, 3, 3, 3, 17, 17, 17, 17] 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: 179 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 524) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000340455734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340455734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340455734 none CCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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: [47, 43, 18, 18, 18, 18, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 47, 47, 47, 47, 47, 43, 43, 18, 18, 3, 3, 3, 3, 18, 18, 18, 18] 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: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340455734 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340455734 Building ZINC000340517812 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340517812 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/525 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340517812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340517812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340517812 none CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 21, 21, 21, 21, 21, 21, 16, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 32, 32, 32, 32, 32, 21, 21, 21, 21, 16, 16, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/526 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340517812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340517812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340517812 none CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 21, 21, 21, 21, 21, 21, 16, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 35, 35, 35, 35, 35, 21, 21, 21, 21, 16, 16, 11, 11, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340517812 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 Building ZINC000340517812 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340517812 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 525) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340517812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340517812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340517812 none CCOc1ccccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 21, 21, 21, 21, 21, 21, 16, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 32, 32, 32, 32, 32, 21, 21, 21, 21, 16, 16, 11, 11, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 526) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340517812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340517812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340517812 none CCOc1ccccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 29, 21, 21, 21, 21, 21, 21, 16, 11, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 35, 35, 35, 35, 35, 21, 21, 21, 21, 16, 16, 11, 11, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340517812 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340517812 Building ZINC000340523109 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340523109 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/527 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340523109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340523109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000340523109 none CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 25, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/528 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340523109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340523109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000340523109 none CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 8, 26, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340523109 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 Building ZINC000340523109 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340523109 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 527) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340523109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340523109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000340523109 none CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 7, 25, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 528) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340523109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340523109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000340523109 none CC(C)(C)OC(=O)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.3', 'N.am', 'C.2', '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, 5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 8, 26, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340523109 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340523109 Building ZINC000340607845 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340607845 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/529 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340607845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340607845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340607845 none CC(=O)Nc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 10, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/530 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340607845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340607845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340607845 none CC(=O)Nc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 9, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340607845 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 Building ZINC000340607845 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340607845 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 529) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(=O)Nc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340607845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340607845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340607845 none CC(=O)Nc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 10, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 530) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(=O)Nc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340607845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340607845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340607845 none CC(=O)Nc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 9, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340607845 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340607845 Building ZINC000190589502 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000190589502 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/531 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/532 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/533 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/533' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/534 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/534' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190589502 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 Building ZINC000190589502 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000190589502 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 531) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 532) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 533) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 534) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190589502 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 Building ZINC000190589502 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000190589502 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 531) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 532) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 533) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 534) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190589502 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 Building ZINC000190589502 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000190589502 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 531) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 532) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 533) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 15, 15, 15, 15, 15, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8] 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: 68 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 534) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1) `ZINC000190589502.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000190589502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000190589502 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(C)(C)C)c3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 11, 11, 1, 1, 1, 2, 8, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 20, 20, 20, 20, 20, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 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: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190589502 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190589502 Building ZINC000340612688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340612688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/535 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC) `ZINC000340612688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340612688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340612688 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [30, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 25, 15, 15, 43, 30, 30, 30, 15, 15, 4, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 43, 43, 43] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/536 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC) `ZINC000340612688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340612688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340612688 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [30, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 25, 15, 15, 43, 30, 30, 30, 15, 15, 4, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 43, 43, 43] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340612688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 Building ZINC000340612688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340612688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 535) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC) `ZINC000340612688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340612688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340612688 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [30, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 25, 15, 15, 43, 30, 30, 30, 15, 15, 4, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 43, 43, 43] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 536) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC) `ZINC000340612688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340612688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000340612688 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(OC)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [30, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 15, 25, 15, 15, 43, 30, 30, 30, 15, 15, 4, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 43, 43, 43] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340612688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340612688 Building ZINC000340615876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340615876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/537 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1) `ZINC000340615876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340615876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340615876 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/538 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1) `ZINC000340615876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340615876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340615876 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340615876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 Building ZINC000340615876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340615876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 537) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1) `ZINC000340615876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340615876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340615876 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 538) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1) `ZINC000340615876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340615876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340615876 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccn(Cc3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340615876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340615876 Building ZINC000340616839 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340616839 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/539 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(Cc2ccccc2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000340616839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340616839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000340616839 none O=C(NCc1ccn(Cc2ccccc2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/540 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(Cc2ccccc2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000340616839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340616839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000340616839 none O=C(NCc1ccn(Cc2ccccc2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340616839 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 Building ZINC000340616839 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340616839 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 539) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(Cc2ccccc2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000340616839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340616839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000340616839 none O=C(NCc1ccn(Cc2ccccc2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 540) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(Cc2ccccc2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000340616839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340616839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000340616839 none O=C(NCc1ccn(Cc2ccccc2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 23, 23, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340616839 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340616839 Building ZINC000340623171 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340623171 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/541 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340623171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623171 none CC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 10, 10, 20, 20, 20, 20, 20, 20, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/542 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340623171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623171 none CC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 10, 22, 22, 22, 22, 22, 22, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340623171 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 Building ZINC000340623171 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340623171 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 541) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340623171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623171 none CC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 10, 10, 20, 20, 20, 20, 20, 20, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 542) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340623171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623171 none CC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 10, 22, 22, 22, 22, 22, 22, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340623171 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623171 Building ZINC000340623182 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340623182 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/543 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340623182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623182 none CC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 9, 9, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/544 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340623182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623182 none CC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 3, 10, 10, 21, 21, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340623182 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 Building ZINC000340623182 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340623182 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 543) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340623182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623182 none CC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 9, 9, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 7, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 544) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000340623182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340623182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340623182 none CC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['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.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'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 3, 10, 10, 21, 21, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340623182 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340623182 Building ZINC000340624688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340624688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/545 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccnc(OC(F)F)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340624688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340624688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340624688 none O=C(NCc1ccnc(OC(F)F)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 12, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 33, 33, 33, 33, 33, 49, 50, 50, 33, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 33, 33, 50, 33, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/546 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccnc(OC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340624688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340624688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340624688 none O=C(NCc1ccnc(OC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 12, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 34, 34, 34, 34, 34, 49, 50, 50, 34, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 34, 34, 50, 34, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340624688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 Building ZINC000340624688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340624688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 545) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCc1ccnc(OC(F)F)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340624688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340624688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340624688 none O=C(NCc1ccnc(OC(F)F)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 12, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 33, 33, 33, 33, 33, 49, 50, 50, 33, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 33, 33, 50, 33, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 546) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCc1ccnc(OC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340624688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340624688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340624688 none O=C(NCc1ccnc(OC(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 12, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 34, 34, 34, 34, 34, 49, 50, 50, 34, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 34, 34, 50, 34, 2, 2, 2, 2] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340624688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340624688 Building ZINC000340654392 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340654392 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/547 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1n[nH]c2c1cccc2Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340654392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000340654392 none O=C(Nc1n[nH]c2c1cccc2Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/548 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1n[nH]c2c1cccc2Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340654392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000340654392 none O=C(Nc1n[nH]c2c1cccc2Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 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, 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340654392 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 Building ZINC000340654392 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340654392 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 547) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1n[nH]c2c1cccc2Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340654392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000340654392 none O=C(Nc1n[nH]c2c1cccc2Cl)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 548) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1n[nH]c2c1cccc2Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000340654392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000340654392 none O=C(Nc1n[nH]c2c1cccc2Cl)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 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, 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340654392 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340654392 Building ZINC000340659105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340659105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/549 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/550 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/551 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/551' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/552 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/552' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340659105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 Building ZINC000340659105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340659105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 549) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 550) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 551) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 552) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340659105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 Building ZINC000340659105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340659105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 549) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 550) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 551) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 552) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340659105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 Building ZINC000340659105 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000340659105 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 549) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 550) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 16, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 551) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 552) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21) `ZINC000340659105.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000340659105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000340659105 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 14, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340659105 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340659105 Building ZINC000340660433 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340660433 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/553 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nccn1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340660433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340660433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340660433 none O=C(NCc1nccn1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 27, 27, 27, 27, 27, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 27, 27, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/554 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nccn1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340660433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340660433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340660433 none O=C(NCc1nccn1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 27, 27, 27, 27, 27, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 27, 27, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340660433 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 Building ZINC000340660433 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340660433 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 553) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCc1nccn1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340660433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340660433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340660433 none O=C(NCc1nccn1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 27, 27, 27, 27, 27, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 27, 27, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 554) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCc1nccn1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000340660433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340660433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000340660433 none O=C(NCc1nccn1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 27, 27, 27, 27, 27, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 27, 27, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340660433 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340660433 Building ZINC000839762449 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839762449 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/555 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839762449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839762449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000839762449 none CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 9, 21, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 5, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/556 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839762449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839762449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000839762449 none CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 10, 25, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 6, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000839762449 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 Building ZINC000839762449 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000839762449 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 555) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839762449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000839762449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000839762449 none CC1(C)SC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 9, 21, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 5, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 556) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC000839762449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000839762449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000839762449 none CC1(C)SC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 10, 25, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 6, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000839762449 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000839762449 Building ZINC000340804464 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340804464 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/557 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1) `ZINC000340804464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340804464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340804464 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 20, 20, 4, 4, 11, 11, 2, 2, 8, 8, 8, 8, 8, 2, 2, 4, 13, 13, 20, 20, 20, 20, 20, 20, 20, 11, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/558 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1) `ZINC000340804464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340804464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340804464 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 14, 20, 20, 5, 5, 12, 12, 2, 2, 7, 7, 7, 7, 7, 2, 2, 5, 14, 14, 20, 20, 20, 20, 20, 20, 20, 12, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340804464 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 Building ZINC000340804464 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340804464 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 557) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1) `ZINC000340804464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340804464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340804464 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 20, 20, 4, 4, 11, 11, 2, 2, 8, 8, 8, 8, 8, 2, 2, 4, 13, 13, 20, 20, 20, 20, 20, 20, 20, 11, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 558) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1) `ZINC000340804464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340804464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000340804464 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cnn(CC(C)C)c2C(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 15, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 14, 20, 20, 5, 5, 12, 12, 2, 2, 7, 7, 7, 7, 7, 2, 2, 5, 14, 14, 20, 20, 20, 20, 20, 20, 20, 12, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340804464 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340804464 Building ZINC000340782556 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340782556 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/559 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1) `ZINC000340782556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000340782556 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 32, 47, 47, 47, 47, 47, 4, 4, 5, 5, 5, 5, 5, 5, 2, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/560 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1) `ZINC000340782556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000340782556 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 26, 45, 45, 45, 45, 45, 4, 4, 5, 5, 5, 5, 5, 5, 2, 4, 4, 42, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340782556 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 Building ZINC000340782556 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340782556 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 559) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1) `ZINC000340782556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000340782556 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 32, 47, 47, 47, 47, 47, 4, 4, 5, 5, 5, 5, 5, 5, 2, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 560) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1) `ZINC000340782556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000340782556 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC3CCCCC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 26, 45, 45, 45, 45, 45, 4, 4, 5, 5, 5, 5, 5, 5, 2, 4, 4, 42, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340782556 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340782556 Building ZINC000340837395 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340837395 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/561 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340837395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837395 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 4, 13, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 37, 37, 47, 47, 47, 47, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 2, 2, 2, 2, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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, 46, 47]) total number of confs: 177 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/562 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340837395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837395 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 10, 4, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 36, 36, 48, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340837395 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 Building ZINC000340837395 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340837395 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 561) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340837395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837395 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 4, 13, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 37, 37, 47, 47, 47, 47, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 2, 2, 2, 2, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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, 46, 47]) total number of confs: 177 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 562) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340837395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837395 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 10, 4, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 36, 36, 48, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340837395 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837395 Building ZINC000340837407 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340837407 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/563 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340837407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837407 none CC(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 12, 4, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 40, 40, 49, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 50, 50, 50, 50, 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, 46, 47]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/564 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340837407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837407 none CC(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 12, 5, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 36, 36, 48, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340837407 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 Building ZINC000340837407 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340837407 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 563) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340837407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837407 none CC(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 12, 4, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 40, 40, 49, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 50, 50, 50, 50, 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, 46, 47]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 564) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C) `ZINC000340837407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340837407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000340837407 none CC(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 12, 5, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 36, 36, 48, 49, 49, 49, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340837407 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340837407 Building ZINC000340904839 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340904839 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/565 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340904839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904839 none CN(C)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 26, 16, 12, 5, 12, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 12, 16, 16, 16, 26, 26, 26, 26, 26, 26, 19, 19, 16, 16, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/566 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340904839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904839 none CN(C)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 18, 11, 5, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 15, 15, 15, 29, 29, 29, 29, 29, 29, 22, 22, 18, 18, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340904839 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 Building ZINC000340904839 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340904839 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 565) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340904839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904839 none CN(C)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 26, 16, 12, 5, 12, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 12, 16, 16, 16, 26, 26, 26, 26, 26, 26, 19, 19, 16, 16, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 566) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(C)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340904839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904839 none CN(C)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 18, 11, 5, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 15, 15, 15, 29, 29, 29, 29, 29, 29, 22, 22, 18, 18, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340904839 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904839 Building ZINC000340904840 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340904840 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/567 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340904840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904840 none CN(C)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 11, 5, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 13, 13, 13, 31, 31, 31, 31, 31, 31, 23, 23, 19, 19, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 155 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/568 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340904840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904840 none CN(C)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 28, 16, 12, 5, 12, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 16, 16, 16, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340904840 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 Building ZINC000340904840 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340904840 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 567) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340904840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904840 none CN(C)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 11, 5, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 11, 13, 13, 13, 31, 31, 31, 31, 31, 31, 23, 23, 19, 19, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 155 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 568) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C) `ZINC000340904840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340904840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000340904840 none CN(C)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 28, 16, 12, 5, 12, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 16, 16, 16, 28, 28, 28, 28, 28, 28, 20, 20, 16, 16, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000340904840 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000340904840 Building ZINC000341034973 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341034973 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/569 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341034973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034973 none O=C(N[C@@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 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, 15, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/570 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341034973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034973 none O=C(N[C@@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 13, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 5, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341034973 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 Building ZINC000341034973 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341034973 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 569) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341034973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034973 none O=C(N[C@@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 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, 15, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 570) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341034973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034973 none O=C(N[C@@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 13, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 5, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341034973 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034973 Building ZINC000341034974 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341034974 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/571 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341034974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034974 none O=C(N[C@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/572 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341034974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034974 none O=C(N[C@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341034974 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 Building ZINC000341034974 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341034974 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 571) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341034974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034974 none O=C(N[C@H]1CCCSC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 1, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 572) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341034974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341034974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000341034974 none O=C(N[C@H]1CCCSC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341034974 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341034974 Building ZINC000185122407 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185122407 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/573 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC000185122407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185122407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000185122407 none Cn1nc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/574 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC000185122407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185122407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000185122407 none Cn1nc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185122407 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 Building ZINC000185122407 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185122407 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 573) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC000185122407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185122407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000185122407 none Cn1nc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 574) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC000185122407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185122407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000185122407 none Cn1nc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185122407 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185122407 Building ZINC000341071167 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341071167 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/575 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/575' -> `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])c1ccc2c(c1)CCC2) `ZINC000341071167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341071167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071167 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 25, 25, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/576 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/576' -> `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])c1ccc2c(c1)CCC2) `ZINC000341071167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341071167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071167 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341071167 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 Building ZINC000341071167 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341071167 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 575) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341071167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341071167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071167 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 25, 25, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 576) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341071167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341071167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071167 none C[C@@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341071167 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071167 Building ZINC000341071168 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341071168 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/577 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/577' -> `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])c1ccc2c(c1)CCC2) `ZINC000341071168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341071168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071168 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 26, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/578 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/578' -> `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])c1ccc2c(c1)CCC2) `ZINC000341071168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341071168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071168 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 14, 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, 19, 19, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341071168 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 Building ZINC000341071168 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341071168 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 577) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341071168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341071168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071168 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 26, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 578) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341071168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341071168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071168 none C[C@H]1CCC[C@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 14, 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, 19, 19, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341071168 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071168 Building ZINC000341071769 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341071769 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/579 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/579' -> `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])c1ccc2c(c1)CCC2) `ZINC000341071769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341071769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071769 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/580 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/580' -> `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])c1ccc2c(c1)CCC2) `ZINC000341071769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341071769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071769 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341071769 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 Building ZINC000341071769 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341071769 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 579) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341071769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341071769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071769 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 580) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341071769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341071769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341071769 none C[C@@H]1CCC[C@@H](C)N1CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341071769 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341071769 Building ZINC000341138019 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341138019 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/581 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1) `ZINC000341138019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341138019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341138019 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 9, 9, 1, 1, 1, 1, 4, 4, 6, 12, 15, 15, 12, 12, 12, 12, 12, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 4, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9] 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/582 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1) `ZINC000341138019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341138019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341138019 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 4, 4, 6, 12, 15, 15, 12, 12, 12, 12, 12, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 4, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341138019 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 Building ZINC000341138019 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341138019 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 581) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1) `ZINC000341138019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341138019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341138019 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 9, 9, 1, 1, 1, 1, 4, 4, 6, 12, 15, 15, 12, 12, 12, 12, 12, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 4, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9] 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 582) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1) `ZINC000341138019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341138019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341138019 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(C(F)F)CCCCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 17, 9, 9, 1, 1, 1, 1, 4, 4, 6, 12, 15, 15, 12, 12, 12, 12, 12, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 4, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341138019 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341138019 Building ZINC000341181854 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181854 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/583 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181854 none O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 20, 26, 26, 28, 28, 1, 1, 1, 8, 8, 14, 14, 8, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 8, 14, 14, 14, 14, 14, 14, 14, 14] 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/584 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181854 none O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 11, 16, 16, 25, 25, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181854 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 Building ZINC000341181854 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181854 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 583) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181854 none O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 20, 26, 26, 28, 28, 1, 1, 1, 8, 8, 14, 14, 8, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 8, 14, 14, 14, 14, 14, 14, 14, 14] 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 584) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181854 none O=C(N1C[C@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 11, 16, 16, 25, 25, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181854 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181854 Building ZINC000341181856 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181856 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/585 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181856 none O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 26, 26, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 26, 26, 26, 26, 26, 6, 11, 11, 11, 11, 11, 11, 11, 11] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/586 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181856 none O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181856 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 Building ZINC000341181856 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181856 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 585) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181856 none O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 26, 26, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 26, 26, 26, 26, 26, 6, 11, 11, 11, 11, 11, 11, 11, 11] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 586) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181856 none O=C(N1C[C@@]2(CCCO2)[C@@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181856 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181856 Building ZINC000341181858 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181858 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/587 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181858 none O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 14, 14, 14, 14, 14, 11, 14, 14, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 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, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/588 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181858 none O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 19, 19, 19, 19, 19, 19, 14, 19, 19, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 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, 43, 44, 45, 46]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181858 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 Building ZINC000341181858 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181858 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 587) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181858 none O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 14, 14, 14, 14, 14, 11, 14, 14, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 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, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 588) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181858 none O=C(N1C[C@@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 19, 19, 19, 19, 19, 19, 14, 19, 19, 22, 22, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 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, 43, 44, 45, 46]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181858 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181858 Building ZINC000341181859 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181859 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/589 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181859 none O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 11, 15, 15, 15, 15, 15, 11, 15, 15, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 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, 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/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/590 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181859 none O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 14, 19, 19, 19, 19, 19, 14, 19, 19, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181859 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 Building ZINC000341181859 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341181859 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 589) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341181859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181859 none O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 11, 15, 15, 15, 15, 15, 11, 15, 15, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 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, 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/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 590) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341181859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341181859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341181859 none O=C(N1C[C@]2(CCCO2)[C@H]1C1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 14, 19, 19, 19, 19, 19, 14, 19, 19, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341181859 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341181859 Building ZINC000568392008 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568392008 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/591 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)C2)cc1) `ZINC000568392008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568392008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000568392008 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)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', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 23, 23, 23, 23, 41, 41, 23, 23, 23, 48, 48, 23, 48, 48, 23, 3, 3, 3, 3, 3, 3, 3, 23, 23, 123, 48, 48, 48, 48, 48, 23, 23, 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, 39, 40, 41, 42, 43]) total number of confs: 376 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/592 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)C2)cc1) `ZINC000568392008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568392008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000568392008 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)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', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 2, 1, 1, 1, 1, 5, 9, 26, 26, 26, 26, 48, 48, 26, 26, 26, 50, 50, 26, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 26, 26, 144, 50, 50, 50, 50, 50, 26, 26, 2, 2] 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, 39, 40, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000568392008 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 Building ZINC000568392008 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000568392008 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 591) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)C2)cc1) `ZINC000568392008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568392008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000568392008 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)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', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 23, 23, 23, 23, 41, 41, 23, 23, 23, 48, 48, 23, 48, 48, 23, 3, 3, 3, 3, 3, 3, 3, 23, 23, 123, 48, 48, 48, 48, 48, 23, 23, 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, 39, 40, 41, 42, 43]) total number of confs: 376 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 592) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)C2)cc1) `ZINC000568392008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568392008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000568392008 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](C(=O)O)[C@@H](c3ccccc3)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', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 2, 1, 1, 1, 1, 5, 9, 26, 26, 26, 26, 48, 48, 26, 26, 26, 50, 50, 26, 50, 50, 26, 2, 2, 2, 2, 2, 2, 2, 26, 26, 144, 50, 50, 50, 50, 50, 26, 26, 2, 2] 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, 39, 40, 41, 42, 43]) total number of confs: 386 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000568392008 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000568392008 Building ZINC000341284138 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341284138 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/593 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341284138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341284138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341284138 none CC(C)OCCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'H'] dock atom type numbers: [5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 27, 19, 14, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 27, 27, 18, 19, 16, 16, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 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: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/594 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341284138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341284138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341284138 none CC(C)OCCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'H'] dock atom type numbers: [5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 27, 19, 14, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 27, 27, 19, 18, 16, 16, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341284138 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 Building ZINC000341284138 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341284138 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 593) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)OCCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341284138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341284138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341284138 none CC(C)OCCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'H'] dock atom type numbers: [5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 27, 19, 14, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 27, 27, 18, 19, 16, 16, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 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: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 594) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)OCCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000341284138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341284138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341284138 none CC(C)OCCCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'H'] dock atom type numbers: [5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 27, 19, 14, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 27, 27, 19, 18, 16, 16, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 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: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341284138 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341284138 Building ZINC000341370311 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370311 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/595 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/595' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370311 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 26, 26, 26, 14, 26, 26, 26, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 14, 14, 26, 19, 26, 9] 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: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/596 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/596' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370311 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 23, 23, 23, 11, 23, 23, 23, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 3, 11, 11, 23, 14, 23, 9] 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370311 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 Building ZINC000341370311 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370311 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 595) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2c(F)cccc2F)cn1) `ZINC000341370311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370311 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 26, 26, 26, 14, 26, 26, 26, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 14, 14, 26, 19, 26, 9] 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: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 596) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2c(F)cccc2F)cn1) `ZINC000341370311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370311 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 23, 23, 23, 11, 23, 23, 23, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 3, 11, 11, 23, 14, 23, 9] 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370311 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370311 Building ZINC000341370339 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370339 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/597 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/597' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370339 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 22, 22, 22, 13, 22, 22, 22, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 13, 13, 22, 13, 22, 9] 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/598 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/598' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370339 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 25, 25, 25, 14, 25, 25, 25, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 14, 14, 25, 14, 25, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370339 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 Building ZINC000341370339 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370339 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 597) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H]2c2c(F)cccc2F)cn1) `ZINC000341370339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370339 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 22, 22, 22, 13, 22, 22, 22, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 13, 13, 22, 13, 22, 9] 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 598) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H]2c2c(F)cccc2F)cn1) `ZINC000341370339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370339 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 25, 25, 25, 14, 25, 25, 25, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 14, 14, 25, 14, 25, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370339 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370339 Building ZINC000341370344 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370344 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/599 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/599' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370344 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 17, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 19, 19, 19, 13, 19, 19, 19, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 4, 13, 13, 19, 13, 19, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/600 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/600' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370344 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 21, 21, 13, 21, 21, 21, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 13, 13, 21, 13, 21, 9] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370344 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 Building ZINC000341370344 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370344 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 599) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H]2c2c(F)cccc2F)cn1) `ZINC000341370344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370344 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 17, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 19, 19, 19, 13, 19, 19, 19, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 4, 13, 13, 19, 13, 19, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 600) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H]2c2c(F)cccc2F)cn1) `ZINC000341370344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370344 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 20, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 21, 21, 13, 21, 21, 21, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 4, 13, 13, 21, 13, 21, 9] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370344 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370344 Building ZINC000341370349 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370349 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/601 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/601' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370349 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 13, 13, 21, 21, 21, 9] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/602 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/602' -> `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]2c2c(F)cccc2F)cn1) `ZINC000341370349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370349 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 19, 19, 19, 13, 19, 19, 19, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 13, 13, 19, 13, 19, 9] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370349 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 Building ZINC000341370349 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341370349 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 601) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@H]2c2c(F)cccc2F)cn1) `ZINC000341370349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341370349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370349 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 13, 13, 21, 21, 21, 9] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 602) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@H]2c2c(F)cccc2F)cn1) `ZINC000341370349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341370349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341370349 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2C[C@@H]2c2c(F)cccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 15, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 19, 19, 19, 13, 19, 19, 19, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 13, 13, 19, 13, 19, 9] 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: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341370349 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341370349 Building ZINC000185584476 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185584476 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/603 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21) `ZINC000185584476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185584476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185584476 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21 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.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 2, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 16, 8, 8, 8, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20] 30 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/604 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21) `ZINC000185584476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185584476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185584476 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21 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.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 2, 8, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 15, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20] 29 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185584476 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 Building ZINC000185584476 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185584476 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 603) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21) `ZINC000185584476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185584476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185584476 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21 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.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 2, 7, 7, 1, 1, 1, 2, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 16, 8, 8, 8, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 20, 20, 20] 30 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 604) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21) `ZINC000185584476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185584476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185584476 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2cccc(OC)c21 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.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 2, 8, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 15, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20] 29 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185584476 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185584476 Building ZINC000341408292 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341408292 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/605 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341408292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408292 none O=C(N1CCOC[C@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 10, 10, 10, 10, 10, 24, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 21, 21, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/606 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341408292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408292 none O=C(N1CCOC[C@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 11, 11, 11, 11, 11, 11, 11, 24, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 20, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341408292 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 Building ZINC000341408292 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341408292 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 605) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341408292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408292 none O=C(N1CCOC[C@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 10, 10, 10, 10, 10, 24, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 21, 21, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 606) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341408292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408292 none O=C(N1CCOC[C@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 11, 11, 11, 11, 11, 11, 11, 24, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 20, 20, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341408292 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408292 Building ZINC000341408293 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341408293 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/607 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341408293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408293 none O=C(N1CCOC[C@@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 12, 12, 12, 12, 12, 12, 12, 20, 28, 28, 28, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 12, 12, 12, 12, 12, 12, 18, 18, 28, 28, 28, 28, 28, 28, 28, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/608 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341408293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408293 none O=C(N1CCOC[C@@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 10, 10, 10, 10, 10, 22, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341408293 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 Building ZINC000341408293 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341408293 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 607) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341408293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408293 none O=C(N1CCOC[C@@H]1CC1CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 12, 12, 12, 12, 12, 12, 12, 20, 28, 28, 28, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 12, 12, 12, 12, 12, 12, 18, 18, 28, 28, 28, 28, 28, 28, 28, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 608) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341408293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341408293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341408293 none O=C(N1CCOC[C@@H]1CC1CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 10, 10, 10, 10, 10, 22, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341408293 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341408293 Building ZINC000341413028 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341413028 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/609 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000341413028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341413028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341413028 none COc1cccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.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, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 15, 15, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 4, 4, 15, 20, 20, 20, 15, 15, 15, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 4, 4, 4, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/610 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000341413028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341413028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341413028 none COc1cccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.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, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 14, 14, 14, 14, 4, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 4, 4, 14, 19, 19, 19, 14, 14, 14, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 4, 4, 4, 4, 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, 46, 47]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341413028 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 Building ZINC000341413028 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341413028 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 609) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000341413028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341413028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341413028 none COc1cccc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.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, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 15, 15, 4, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 4, 4, 15, 20, 20, 20, 15, 15, 15, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 4, 4, 4, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 610) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1) `ZINC000341413028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341413028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000341413028 none COc1cccc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.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, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 14, 14, 14, 14, 4, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 4, 4, 14, 19, 19, 19, 14, 14, 14, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 4, 4, 4, 4, 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, 46, 47]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341413028 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341413028 Building ZINC000185649635 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185649635 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/611 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000185649635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185649635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185649635 none COc1ccc(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 43, 43, 43, 43, 43, 43, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 50, 50, 50, 43, 43, 43, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/612 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000185649635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185649635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185649635 none COc1ccc(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 43, 43, 15, 43, 43, 43, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 50, 50, 50, 43, 43, 43, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 210 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185649635 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 Building ZINC000185649635 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185649635 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 611) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000185649635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185649635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185649635 none COc1ccc(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 43, 43, 43, 43, 43, 43, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 50, 50, 50, 43, 43, 43, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 612) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000185649635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185649635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185649635 none COc1ccc(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 43, 43, 15, 43, 43, 43, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 50, 50, 50, 43, 43, 43, 15, 15, 3, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 210 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185649635 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185649635 Building ZINC000341489151 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341489151 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/613 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1) `ZINC000341489151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341489151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000341489151 none Cc1ncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 10, 10, 21, 21, 10, 10, 10, 10, 10, 4, 9, 17, 17, 9, 17, 17, 9, 21, 21, 21, 21, 21] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/614 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1) `ZINC000341489151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341489151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000341489151 none Cc1ncc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 7, 7, 23, 23, 7, 7, 7, 7, 7, 4, 9, 18, 18, 9, 18, 18, 9, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341489151 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 Building ZINC000341489151 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341489151 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 613) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1) `ZINC000341489151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341489151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000341489151 none Cc1ncc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 10, 10, 21, 21, 10, 10, 10, 10, 10, 4, 9, 17, 17, 9, 17, 17, 9, 21, 21, 21, 21, 21] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 614) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ncc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1) `ZINC000341489151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341489151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000341489151 none Cc1ncc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 7, 7, 23, 23, 7, 7, 7, 7, 7, 4, 9, 18, 18, 9, 18, 18, 9, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341489151 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341489151 Building ZINC000341607478 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341607478 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/615 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F) `ZINC000341607478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341607478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000341607478 none CCn1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 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: [49, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 29, 6, 6, 6, 6, 6] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/616 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F) `ZINC000341607478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341607478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000341607478 none CCn1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 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: [49, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 29, 6, 6, 6, 6, 6] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341607478 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 Building ZINC000341607478 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341607478 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 615) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F) `ZINC000341607478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341607478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000341607478 none CCn1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 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: [49, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 29, 6, 6, 6, 6, 6] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 616) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F) `ZINC000341607478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341607478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000341607478 none CCn1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 15, 15, 15, 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: [49, 29, 29, 29, 29, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 29, 6, 6, 6, 6, 6] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341607478 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341607478 Building ZINC000185892431 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000185892431 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/617 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 39, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/618 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/619 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/619' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 38, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/620 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/620' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 38, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 37, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185892431 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 Building ZINC000185892431 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000185892431 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 617) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 39, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 618) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 619) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 38, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 620) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 38, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 37, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185892431 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 Building ZINC000185892431 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000185892431 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 617) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 39, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 618) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 619) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 38, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 620) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 38, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 37, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185892431 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 Building ZINC000185892431 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000185892431 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 617) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 39, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 618) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 39, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 619) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 43, 43, 38, 43, 43, 24, 24, 3, 3, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 43, 43, 40, 43, 43, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 620) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CC[N@@](c2ccccc2)CC1) `ZINC000185892431.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000185892431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000185892431 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 8, 25, 25, 25, 25, 25, 43, 43, 38, 43, 43, 25, 25, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 43, 43, 37, 43, 43, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185892431 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185892431 Building ZINC000341637815 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341637815 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/621 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C) `ZINC000341637815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341637815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000341637815 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C 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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 14, 14, 8, 12, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 8, 14, 14, 8, 14, 14, 8, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/622 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C) `ZINC000341637815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341637815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000341637815 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C 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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 13, 20, 20, 20, 20, 20, 20, 18, 18, 18, 18, 18, 6, 13, 13, 13, 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: 126 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341637815 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 Building ZINC000341637815 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341637815 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 621) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C) `ZINC000341637815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341637815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000341637815 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C 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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 14, 14, 8, 12, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 8, 14, 14, 8, 14, 14, 8, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 622) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C) `ZINC000341637815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341637815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000341637815 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ncccc1C 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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 13, 20, 20, 20, 20, 20, 20, 18, 18, 18, 18, 18, 6, 13, 13, 13, 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: 126 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341637815 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341637815 Building ZINC000341640366 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640366 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/623 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/624 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/625 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/625' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/626 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/626' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640366 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 Building ZINC000341640366 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640366 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 623) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 624) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 625) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 626) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640366 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 Building ZINC000341640366 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640366 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 623) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 624) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 625) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 626) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640366 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 Building ZINC000341640366 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640366 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 623) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 624) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 625) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 626) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640366 none O=C(N[C@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640366 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640366 Building ZINC000341640372 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640372 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/627 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/628 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/629 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/629' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/630 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/630' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640372 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 Building ZINC000341640372 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640372 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 627) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 628) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 629) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 630) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640372 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 Building ZINC000341640372 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640372 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 627) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 628) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 629) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 630) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640372 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 Building ZINC000341640372 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000341640372 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 627) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 628) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 629) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 630) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341640372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000341640372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341640372 none O=C(N[C@@H]1CCCN(c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341640372 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341640372 Building ZINC000185934669 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185934669 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/631 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185934669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185934669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185934669 none O=C(N1CCC(O)(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 19, 19, 19, 19, 19, 28, 28, 19, 28, 28, 19, 19, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 19, 19, 19, 19, 57, 28, 28, 19, 28, 28, 19, 19, 19, 19, 6, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/632 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185934669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185934669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185934669 none O=C(N1CCC(O)(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 18, 18, 18, 18, 18, 27, 27, 18, 27, 27, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 54, 27, 27, 18, 27, 27, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185934669 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 Building ZINC000185934669 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185934669 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 631) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCC(O)(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185934669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185934669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185934669 none O=C(N1CCC(O)(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 19, 19, 19, 19, 19, 28, 28, 19, 28, 28, 19, 19, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 19, 19, 19, 19, 57, 28, 28, 19, 28, 28, 19, 19, 19, 19, 6, 8, 8, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 632) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N1CCC(O)(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185934669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185934669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185934669 none O=C(N1CCC(O)(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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: [6, 9, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 18, 18, 18, 18, 18, 27, 27, 18, 27, 27, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 54, 27, 27, 18, 27, 27, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185934669 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185934669 Building ZINC000185961593 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185961593 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/633 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1Cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O) `ZINC000185961593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185961593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000185961593 none CN1Cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/634 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1Cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O) `ZINC000185961593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185961593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000185961593 none CN1Cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185961593 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 Building ZINC000185961593 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185961593 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 633) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1Cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O) `ZINC000185961593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185961593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000185961593 none CN1Cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 634) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN1Cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O) `ZINC000185961593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185961593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000185961593 none CN1Cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185961593 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185961593 Building ZINC000765320505 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000765320505 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/635 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000765320505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000765320505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000765320505 none C[C@@H](C[C@H](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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 38, 38, 150, 50, 50, 50, 50, 5, 3, 3, 3, 3] 150 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 391 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/636 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C[C@H](O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000765320505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000765320505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000765320505 none C[C@@H](C[C@H](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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 16, 33, 47, 47, 47, 49, 49, 47, 47, 49, 49, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 16, 16, 38, 38, 141, 49, 49, 49, 49, 5, 4, 4, 4, 4] 150 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 377 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000765320505 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 Building ZINC000765320505 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000765320505 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 635) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](C[C@H](O)c1ccc(F)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000765320505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000765320505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000765320505 none C[C@@H](C[C@H](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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 38, 38, 150, 50, 50, 50, 50, 5, 3, 3, 3, 3] 150 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 391 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 636) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](C[C@H](O)c1ccc(F)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000765320505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000765320505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000765320505 none C[C@@H](C[C@H](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.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 16, 33, 47, 47, 47, 49, 49, 47, 47, 49, 49, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 16, 16, 38, 38, 141, 49, 49, 49, 49, 5, 4, 4, 4, 4] 150 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 377 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000765320505 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000765320505 Building ZINC000185982646 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185982646 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/637 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[S@@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185982646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982646 none C[S@@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 10, 10, 10, 4, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 20, 20, 10, 4, 10, 10, 4, 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]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/638 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[S@@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185982646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982646 none C[S@@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 24, 11, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 11, 3, 11, 11, 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]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185982646 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 Building ZINC000185982646 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185982646 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 637) grep: /scratch/xiaobo/25650/xaq-8058115.17/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[S@@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185982646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982646 none C[S@@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 10, 10, 10, 4, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 20, 20, 10, 4, 10, 10, 4, 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]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 638) grep: /scratch/xiaobo/25650/xaq-8058115.17/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[S@@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185982646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982646 none C[S@@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 24, 11, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 11, 3, 11, 11, 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]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185982646 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982646 Building ZINC000185982667 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185982667 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/639 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[S@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185982667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982667 none C[S@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 24, 11, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 11, 3, 11, 11, 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]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/640 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[S@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185982667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982667 none C[S@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 10, 10, 10, 4, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 20, 20, 10, 4, 10, 10, 4, 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]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185982667 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 Building ZINC000185982667 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185982667 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 639) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[S@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185982667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982667 none C[S@](=O)Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 19, 24, 11, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 11, 3, 11, 11, 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]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 640) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[S@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000185982667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185982667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000185982667 none C[S@](=O)Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 23, 10, 10, 10, 4, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 20, 20, 10, 4, 10, 10, 4, 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]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000185982667 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000185982667 Building ZINC000341709175 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341709175 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/641 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000341709175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341709175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000341709175 none CN(C)CCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 22, 12, 2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 12, 12, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12, 12, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/642 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000341709175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341709175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000341709175 none CN(C)CCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 10, 2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 10, 10, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 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, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341709175 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 Building ZINC000341709175 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341709175 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 641) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000341709175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341709175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000341709175 none CN(C)CCc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 22, 12, 2, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 12, 12, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12, 12, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 642) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000341709175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341709175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000341709175 none CN(C)CCc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 10, 2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 10, 10, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 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, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341709175 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341709175 Building ZINC000341724571 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341724571 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/643 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341724571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341724571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000341724571 none COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 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, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 27, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 48, 48, 8, 8, 8, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/644 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341724571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341724571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000341724571 none COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 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, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 27, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 47, 47, 8, 8, 8, 4, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341724571 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 Building ZINC000341724571 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341724571 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 643) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341724571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341724571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000341724571 none COCCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 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, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 27, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 48, 48, 8, 8, 8, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 644) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341724571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341724571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000341724571 none COCCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 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, 6, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 27, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 47, 47, 8, 8, 8, 4, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341724571 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341724571 Building ZINC000070806685 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806685 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/645 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806685 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 6, 21, 21, 21, 21, 21, 21, 21, 12, 18, 18, 12, 18, 18, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/646 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806685 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 5, 18, 18, 18, 18, 18, 18, 18, 10, 17, 17, 17, 17, 17, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806685 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 Building ZINC000070806685 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806685 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 645) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806685 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 6, 21, 21, 21, 21, 21, 21, 21, 12, 18, 18, 12, 18, 18, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 646) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806685 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 5, 18, 18, 18, 18, 18, 18, 18, 10, 17, 17, 17, 17, 17, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806685 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806685 Building ZINC000070806686 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806686 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/647 `/scratch/xiaobo/25650/xaq-8058115.17/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]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806686 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 14, 14, 27, 27, 18, 27, 27, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 4, 14, 14, 27, 27, 27, 27, 27, 10, 12, 12, 10, 12, 12, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/648 `/scratch/xiaobo/25650/xaq-8058115.17/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]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806686 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 23, 23, 18, 23, 23, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 13, 13, 23, 23, 23, 23, 23, 10, 15, 15, 10, 15, 15, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806686 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 Building ZINC000070806686 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806686 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 647) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806686 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 14, 14, 27, 27, 18, 27, 27, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 4, 14, 14, 27, 27, 27, 27, 27, 10, 12, 12, 10, 12, 12, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 648) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806686 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 23, 23, 18, 23, 23, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 13, 13, 23, 23, 23, 23, 23, 10, 15, 15, 10, 15, 15, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806686 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806686 Building ZINC000070806688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/649 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806688 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 12, 12, 24, 24, 12, 24, 24, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 4, 12, 12, 24, 24, 12, 24, 24, 10, 16, 16, 10, 16, 16, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/650 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806688 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 14, 14, 28, 28, 14, 28, 28, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 4, 14, 14, 28, 28, 14, 28, 28, 9, 15, 15, 9, 15, 15, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 Building ZINC000070806688 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806688 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 649) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806688 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 12, 12, 24, 24, 12, 24, 24, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 4, 12, 12, 24, 24, 12, 24, 24, 10, 16, 16, 10, 16, 16, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 650) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806688 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 14, 14, 28, 28, 14, 28, 28, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 4, 14, 14, 28, 28, 14, 28, 28, 9, 15, 15, 9, 15, 15, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806688 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806688 Building ZINC000070806690 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806690 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/651 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806690 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 5, 17, 17, 17, 17, 17, 17, 17, 9, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/652 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806690 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 6, 21, 21, 21, 21, 21, 21, 21, 12, 18, 18, 13, 18, 18, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806690 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 Building ZINC000070806690 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070806690 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 651) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070806690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806690 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 5, 17, 17, 17, 17, 17, 17, 17, 9, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 652) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070806690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070806690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000070806690 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 6, 21, 21, 21, 21, 21, 21, 21, 12, 18, 18, 13, 18, 18, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/25650/xaq-8058115.17/working/building/ZINC000070806690 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070806690 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070806690 Building ZINC000186092792 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186092792 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/653 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C) `ZINC000186092792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186092792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092792 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/654 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C) `ZINC000186092792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186092792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092792 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 16, 16, 22, 22, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 6, 6, 6, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186092792 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 Building ZINC000186092792 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186092792 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 653) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C) `ZINC000186092792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186092792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092792 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 654) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C) `ZINC000186092792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186092792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092792 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 16, 16, 22, 22, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 6, 6, 6, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186092792 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092792 Building ZINC000186092805 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186092805 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/655 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C) `ZINC000186092805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186092805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092805 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 13, 13, 17, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/656 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C) `ZINC000186092805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186092805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092805 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 18, 18, 18, 18, 18, 18, 18, 32, 32, 32, 32, 32, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 32, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186092805 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 Building ZINC000186092805 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186092805 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 655) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C) `ZINC000186092805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186092805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092805 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 13, 13, 17, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 656) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C) `ZINC000186092805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186092805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000186092805 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1cccn1C 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', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 18, 18, 18, 18, 18, 18, 18, 32, 32, 32, 32, 32, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 32, 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, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186092805 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186092805 Building ZINC000341786812 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341786812 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/657 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCC)CCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341786812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341786812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000341786812 none CCCN(CCC)CCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 16, 24, 24, 26, 13, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 24, 24, 24, 24, 26, 26, 26, 26, 26, 16, 16, 16, 16, 9, 9, 2, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/658 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCC)CCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341786812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341786812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000341786812 none CCCN(CCC)CCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 18, 26, 26, 28, 15, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 26, 26, 26, 26, 28, 28, 28, 28, 28, 18, 18, 17, 17, 10, 10, 2, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341786812 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 Building ZINC000341786812 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341786812 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 657) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCC)CCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341786812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341786812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000341786812 none CCCN(CCC)CCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 16, 24, 24, 26, 13, 9, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 24, 24, 24, 24, 26, 26, 26, 26, 26, 16, 16, 16, 16, 9, 9, 2, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 658) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCC)CCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000341786812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341786812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000341786812 none CCCN(CCC)CCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 18, 26, 26, 28, 15, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 26, 26, 26, 26, 28, 28, 28, 28, 28, 18, 18, 17, 17, 10, 10, 2, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341786812 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341786812 Building ZINC000341799807 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341799807 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/659 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341799807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341799807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000341799807 none Cn1nc(CC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 20, 20, 20, 20, 12, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 7, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/660 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341799807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341799807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000341799807 none Cn1nc(CC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 22, 22, 22, 22, 13, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 8, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341799807 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 Building ZINC000341799807 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341799807 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 659) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nc(CC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341799807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341799807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000341799807 none Cn1nc(CC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 20, 20, 20, 20, 12, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 7, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 660) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1nc(CC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341799807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341799807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000341799807 none Cn1nc(CC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 22, 22, 22, 22, 13, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 8, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341799807 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341799807 Building ZINC000070842216 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070842216 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/661 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070842216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842216 none Cc1csc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 30, 30, 6, 6, 6, 4, 6, 7, 7, 7, 7, 7, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/662 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070842216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842216 none Cc1csc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070842216 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 Building ZINC000070842216 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070842216 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 661) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1csc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070842216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842216 none Cc1csc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 30, 30, 6, 6, 6, 4, 6, 7, 7, 7, 7, 7, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 662) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1csc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070842216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842216 none Cc1csc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070842216 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842216 Building ZINC000070842221 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070842221 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/663 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070842221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842221 none Cc1csc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/664 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070842221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842221 none Cc1csc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 30, 30, 6, 6, 6, 4, 6, 7, 7, 6, 7, 7, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070842221 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 Building ZINC000070842221 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070842221 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 663) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1csc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070842221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842221 none Cc1csc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 5, 5, 5, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 664) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1csc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1) `ZINC000070842221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070842221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000070842221 none Cc1csc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 30, 30, 6, 6, 6, 4, 6, 7, 7, 6, 7, 7, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070842221 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070842221 Building ZINC000341819102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341819102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/665 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1) `ZINC000341819102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341819102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000341819102 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 8, 1, 8, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 10, 44, 88, 44, 44, 6, 6] 100 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/666 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1) `ZINC000341819102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341819102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000341819102 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 8, 1, 8, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 6, 6, 1, 1, 1, 1, 10, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 10, 44, 88, 44, 44, 6, 6] 100 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341819102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 Building ZINC000341819102 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341819102 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 665) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1) `ZINC000341819102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341819102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000341819102 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 8, 1, 8, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 10, 44, 88, 44, 44, 6, 6] 100 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 666) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1) `ZINC000341819102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341819102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000341819102 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc3c(O)ncnc3cc2F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 8, 1, 8, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 6, 6, 1, 1, 1, 1, 10, 10, 10, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 10, 44, 88, 44, 44, 6, 6] 100 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341819102 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341819102 Building ZINC000341823060 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341823060 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/667 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1F)CCNC2=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341823060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341823060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341823060 none O=C(Nc1ccc2c(c1F)CCNC2=O)[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.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 39, 45, 45, 45, 39, 45, 45, 45, 45, 45, 45, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/668 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1F)CCNC2=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341823060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341823060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341823060 none O=C(Nc1ccc2c(c1F)CCNC2=O)[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.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 39, 45, 45, 45, 39, 45, 45, 45, 45, 45, 45, 1, 1, 1, 6, 6, 1, 6, 6, 6, 9, 45, 45, 45, 45, 45, 45, 45, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341823060 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 Building ZINC000341823060 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341823060 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 667) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(Nc1ccc2c(c1F)CCNC2=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341823060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341823060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341823060 none O=C(Nc1ccc2c(c1F)CCNC2=O)[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.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 39, 45, 45, 45, 39, 45, 45, 45, 45, 45, 45, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 668) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(Nc1ccc2c(c1F)CCNC2=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000341823060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341823060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000341823060 none O=C(Nc1ccc2c(c1F)CCNC2=O)[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.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 39, 45, 45, 45, 39, 45, 45, 45, 45, 45, 45, 1, 1, 1, 6, 6, 1, 6, 6, 6, 9, 45, 45, 45, 45, 45, 45, 45, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341823060 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341823060 Building ZINC000341837640 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341837640 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/669 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)cc1Cl) `ZINC000341837640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341837640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341837640 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 25, 25, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 16, 16, 25, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/670 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)cc1Cl) `ZINC000341837640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341837640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341837640 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 25, 25, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 16, 16, 25, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341837640 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 Building ZINC000341837640 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341837640 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 669) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)cc1Cl) `ZINC000341837640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341837640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341837640 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 25, 25, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 16, 16, 25, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 670) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)cc1Cl) `ZINC000341837640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341837640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341837640 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnc(CC3CC3)nc2)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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 25, 25, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 16, 16, 25, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341837640 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341837640 Building ZINC000070852713 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070852713 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/671 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1ccccc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070852713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070852713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000070852713 none O=C(N[C@@H]1C[C@H]1c1ccccc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 27, 27, 13, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 4, 13, 13, 27, 27, 26, 27, 9, 13, 13, 9, 13, 13, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/672 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1ccccc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070852713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070852713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000070852713 none O=C(N[C@@H]1C[C@H]1c1ccccc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 30, 30, 14, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 4, 13, 13, 30, 30, 30, 30, 9, 13, 13, 9, 13, 13, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070852713 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 Building ZINC000070852713 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000070852713 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 671) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N[C@@H]1C[C@H]1c1ccccc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070852713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000070852713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000070852713 none O=C(N[C@@H]1C[C@H]1c1ccccc1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 27, 27, 13, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 4, 13, 13, 27, 27, 26, 27, 9, 13, 13, 9, 13, 13, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 672) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N[C@@H]1C[C@H]1c1ccccc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000070852713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000070852713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000070852713 none O=C(N[C@@H]1C[C@H]1c1ccccc1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 13, 13, 30, 30, 14, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 13, 13, 9, 4, 13, 13, 30, 30, 30, 30, 9, 13, 13, 9, 13, 13, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000070852713 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000070852713 Building ZINC000341846740 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341846740 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/673 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341846740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846740 none COC(=O)[C@@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [28, 28, 18, 28, 9, 18, 18, 4, 9, 19, 24, 24, 22, 24, 24, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 18, 18, 18, 19, 19, 24, 24, 24, 24, 24, 3, 3, 3, 3] 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: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/674 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341846740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846740 none COC(=O)[C@@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 20, 32, 9, 20, 20, 4, 9, 25, 30, 30, 28, 30, 30, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 20, 20, 20, 25, 25, 30, 30, 30, 30, 30, 3, 3, 3, 3] 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341846740 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 Building ZINC000341846740 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341846740 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 673) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)[C@@H](C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341846740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846740 none COC(=O)[C@@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [28, 28, 18, 28, 9, 18, 18, 4, 9, 19, 24, 24, 22, 24, 24, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 18, 18, 18, 19, 19, 24, 24, 24, 24, 24, 3, 3, 3, 3] 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: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 674) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)[C@@H](C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341846740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846740 none COC(=O)[C@@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 20, 32, 9, 20, 20, 4, 9, 25, 30, 30, 28, 30, 30, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 20, 20, 20, 25, 25, 30, 30, 30, 30, 30, 3, 3, 3, 3] 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341846740 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846740 Building ZINC000341846741 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341846741 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/675 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341846741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846741 none COC(=O)[C@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 33, 21, 33, 10, 21, 21, 4, 10, 25, 29, 29, 27, 29, 29, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 21, 21, 21, 25, 25, 29, 29, 29, 29, 29, 3, 3, 3, 3] 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: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/676 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341846741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846741 none COC(=O)[C@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [28, 28, 18, 28, 9, 18, 18, 4, 9, 19, 24, 24, 21, 24, 24, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 18, 18, 18, 19, 19, 24, 24, 24, 24, 24, 3, 3, 3, 3] 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: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341846741 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 Building ZINC000341846741 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341846741 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 675) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)[C@H](C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341846741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846741 none COC(=O)[C@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 33, 21, 33, 10, 21, 21, 4, 10, 25, 29, 29, 27, 29, 29, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 21, 21, 21, 25, 25, 29, 29, 29, 29, 29, 3, 3, 3, 3] 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: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 676) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)[C@H](C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341846741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341846741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000341846741 none COC(=O)[C@H](C)N(Cc1ccccc1)C(=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', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [28, 28, 18, 28, 9, 18, 18, 4, 9, 19, 24, 24, 21, 24, 24, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 18, 18, 18, 19, 19, 24, 24, 24, 24, 24, 3, 3, 3, 3] 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: 173 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341846741 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341846741 Building ZINC000186197744 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186197744 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/677 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1) `ZINC000186197744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186197744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000186197744 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 10, 21, 48, 50, 50, 48, 48, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/678 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1) `ZINC000186197744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186197744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000186197744 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 10, 21, 47, 50, 50, 47, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186197744 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 Building ZINC000186197744 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186197744 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 677) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1) `ZINC000186197744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186197744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000186197744 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 10, 21, 48, 50, 50, 48, 48, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 48, 48, 50, 50, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 678) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1) `ZINC000186197744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186197744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000186197744 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCOCc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 10, 21, 47, 50, 50, 47, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 10, 10, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186197744 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186197744 Building ZINC000186185212 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186185212 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/679 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c1) `ZINC000186185212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186185212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000186185212 none CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 24, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 50, 50, 50, 50, 50, 34, 34, 34, 24, 24, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/680 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c1) `ZINC000186185212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186185212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000186185212 none CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 23, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 50, 50, 50, 50, 50, 34, 34, 34, 23, 23, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186185212 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 Building ZINC000186185212 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186185212 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 679) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c1) `ZINC000186185212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186185212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000186185212 none CCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 24, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 50, 50, 50, 50, 50, 34, 34, 34, 24, 24, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 680) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c1) `ZINC000186185212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186185212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000186185212 none CCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 23, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 34, 50, 50, 50, 50, 50, 34, 34, 34, 23, 23, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186185212 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186185212 Building ZINC000341862210 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341862210 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/681 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341862210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341862210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341862210 none CCOc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 12, 12, 12, 12, 12, 12, 8, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 40, 40, 40, 40, 40, 12, 12, 12, 12, 8, 8, 3, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/682 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341862210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341862210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341862210 none CCOc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 13, 13, 13, 12, 13, 13, 8, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 41, 41, 41, 41, 41, 13, 13, 13, 13, 8, 8, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341862210 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 Building ZINC000341862210 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341862210 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 681) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341862210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341862210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341862210 none CCOc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 12, 12, 12, 12, 12, 12, 8, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 40, 40, 40, 40, 40, 12, 12, 12, 12, 8, 8, 3, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 682) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCOc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000341862210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341862210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000341862210 none CCOc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 13, 13, 13, 12, 13, 13, 8, 3, 2, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 41, 41, 41, 41, 41, 13, 13, 13, 13, 8, 8, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341862210 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862210 Building ZINC000341862801 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341862801 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/683 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/683' -> `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(CC(F)F)CC2CCC2)cn1) `ZINC000341862801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341862801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341862801 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC(F)F)CC2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 14, 14, 4, 12, 18, 18, 18, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 9, 9, 14, 8, 8, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/684 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/684' -> `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(CC(F)F)CC2CCC2)cn1) `ZINC000341862801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341862801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341862801 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC(F)F)CC2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 15, 15, 4, 12, 21, 21, 21, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 9, 9, 15, 9, 9, 21, 21, 21, 21, 21, 21, 21, 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341862801 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 Building ZINC000341862801 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341862801 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 683) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC(F)F)CC2CCC2)cn1) `ZINC000341862801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341862801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341862801 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CC(F)F)CC2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 14, 14, 4, 12, 18, 18, 18, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 9, 9, 14, 8, 8, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 684) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC(F)F)CC2CCC2)cn1) `ZINC000341862801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341862801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000341862801 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CC(F)F)CC2CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 15, 15, 4, 12, 21, 21, 21, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 9, 9, 15, 9, 9, 21, 21, 21, 21, 21, 21, 21, 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341862801 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341862801 Building ZINC000341864027 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341864027 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/685 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)F)CC1CCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000341864027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341864027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000341864027 none O=C(N(CC(F)F)CC1CCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 5, 14, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 11, 11, 17, 11, 11, 21, 21, 21, 21, 21, 21, 21, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/686 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)F)CC1CCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000341864027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341864027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000341864027 none O=C(N(CC(F)F)CC1CCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 5, 13, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 11, 11, 18, 11, 11, 20, 20, 20, 20, 20, 20, 20, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341864027 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 Building ZINC000341864027 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341864027 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 685) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N(CC(F)F)CC1CCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000341864027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341864027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000341864027 none O=C(N(CC(F)F)CC1CCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 5, 14, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 11, 11, 17, 11, 11, 21, 21, 21, 21, 21, 21, 21, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 686) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N(CC(F)F)CC1CCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000341864027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341864027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000341864027 none O=C(N(CC(F)F)CC1CCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 5, 13, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 11, 11, 18, 11, 11, 20, 20, 20, 20, 20, 20, 20, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341864027 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341864027 Building ZINC000190878430 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190878430 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/687 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)c(C)c2)cc1) `ZINC000190878430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190878430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190878430 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)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.3', 'C.ar', 'O.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 12, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 21, 37, 40, 40, 40, 37, 37, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 37, 37, 40, 40, 40, 40, 80, 40, 40, 40, 40, 6, 6] 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: 269 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/688 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)c(C)c2)cc1) `ZINC000190878430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190878430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190878430 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)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.3', 'C.ar', 'O.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 12, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 3, 19, 33, 40, 40, 40, 36, 36, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 3, 19, 19, 33, 33, 40, 40, 40, 40, 80, 40, 40, 40, 40, 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: 264 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190878430 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 Building ZINC000190878430 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190878430 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 687) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)c(C)c2)cc1) `ZINC000190878430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190878430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190878430 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)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.3', 'C.ar', 'O.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 12, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 21, 37, 40, 40, 40, 37, 37, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 37, 37, 40, 40, 40, 40, 80, 40, 40, 40, 40, 6, 6] 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: 269 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 688) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)c(C)c2)cc1) `ZINC000190878430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190878430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190878430 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(C)c(O)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.3', 'C.ar', 'O.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 5, 1, 12, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 3, 19, 33, 40, 40, 40, 36, 36, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6, 3, 19, 19, 33, 33, 40, 40, 40, 40, 80, 40, 40, 40, 40, 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: 264 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190878430 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190878430 Building ZINC000341907157 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341907157 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/689 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1F) `ZINC000341907157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341907157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000341907157 none CNC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 50, 50, 50, 50, 48, 15, 3, 3, 3, 3, 3, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/690 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1F) `ZINC000341907157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341907157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000341907157 none CNC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 50, 50, 50, 50, 48, 15, 3, 3, 3, 3, 3, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341907157 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 Building ZINC000341907157 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341907157 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 689) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CNC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1F) `ZINC000341907157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341907157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000341907157 none CNC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 50, 50, 50, 50, 48, 15, 3, 3, 3, 3, 3, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 690) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CNC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1F) `ZINC000341907157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341907157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000341907157 none CNC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 15, 50, 50, 50, 50, 48, 15, 3, 3, 3, 3, 3, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341907157 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341907157 Building ZINC000341927279 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341927279 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/691 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cnn(c3ccccc3)c2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341927279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341927279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000341927279 none O=C(N1Cc2cnn(c3ccccc3)c2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 18, 18, 18, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 6, 6, 6, 6] 43 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/692 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cnn(c3ccccc3)c2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341927279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341927279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000341927279 none O=C(N1Cc2cnn(c3ccccc3)c2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 18, 18, 18, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 6, 6, 6, 6] 43 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341927279 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 Building ZINC000341927279 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341927279 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 691) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1Cc2cnn(c3ccccc3)c2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341927279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341927279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000341927279 none O=C(N1Cc2cnn(c3ccccc3)c2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 18, 18, 18, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 6, 6, 6, 6] 43 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 692) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1Cc2cnn(c3ccccc3)c2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000341927279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341927279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000341927279 none O=C(N1Cc2cnn(c3ccccc3)c2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 18, 18, 18, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 6, 6, 6, 6] 43 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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/25650/xaq-8058115.17/working/building/ZINC000341927279 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341927279 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341927279 Building ZINC000341959188 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341959188 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/693 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/693' -> `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(=O)Cc1ccccc1) `ZINC000341959188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341959188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959188 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 29, 29, 29, 29, 29, 29, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/694 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/694' -> `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(=O)Cc1ccccc1) `ZINC000341959188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341959188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959188 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 6, 19, 19, 30, 30, 30, 30, 30, 30, 6, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341959188 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 Building ZINC000341959188 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341959188 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 693) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)Cc1ccccc1) `ZINC000341959188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341959188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959188 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 29, 29, 29, 29, 29, 29, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 694) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)Cc1ccccc1) `ZINC000341959188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341959188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959188 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 6, 19, 19, 30, 30, 30, 30, 30, 30, 6, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341959188 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959188 Building ZINC000341959190 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341959190 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/695 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/695' -> `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(=O)Cc1ccccc1) `ZINC000341959190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341959190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 6, 18, 18, 29, 29, 29, 29, 29, 29, 6, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/696 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/696' -> `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(=O)Cc1ccccc1) `ZINC000341959190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341959190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 30, 30, 30, 30, 30, 30, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341959190 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 Building ZINC000341959190 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341959190 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 695) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)Cc1ccccc1) `ZINC000341959190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341959190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 6, 18, 18, 29, 29, 29, 29, 29, 29, 6, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 696) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)Cc1ccccc1) `ZINC000341959190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341959190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341959190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 6, 20, 20, 30, 30, 30, 30, 30, 30, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341959190 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341959190 Building ZINC000341979449 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341979449 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/697 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/697' -> `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)cc1)C(=O)Cc1ccccc1) `ZINC000341979449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341979449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979449 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 27, 27, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/698 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/698' -> `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)cc1)C(=O)Cc1ccccc1) `ZINC000341979449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341979449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979449 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 29, 29, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341979449 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 Building ZINC000341979449 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341979449 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 697) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(=O)Cc1ccccc1) `ZINC000341979449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341979449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979449 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 27, 27, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 698) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(=O)Cc1ccccc1) `ZINC000341979449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341979449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979449 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 29, 29, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341979449 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979449 Building ZINC000341979450 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341979450 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/699 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/699' -> `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)cc1)C(=O)Cc1ccccc1) `ZINC000341979450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341979450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979450 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 29, 29, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/700 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/700' -> `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)cc1)C(=O)Cc1ccccc1) `ZINC000341979450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341979450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979450 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 27, 27, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341979450 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 Building ZINC000341979450 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000341979450 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 699) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(=O)Cc1ccccc1) `ZINC000341979450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000341979450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979450 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 29, 29, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 700) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(=O)Cc1ccccc1) `ZINC000341979450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000341979450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000341979450 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 27, 27, 50, 50, 50, 50, 50, 50, 7, 7, 7, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000341979450 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000341979450 Building ZINC000342002224 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342002224 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/701 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342002224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342002224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342002224 none CC[C@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 4, 13, 13, 30, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 18, 18, 30, 30, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/702 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342002224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342002224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342002224 none CC[C@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [16, 12, 4, 12, 12, 28, 38, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 19, 19, 19, 28, 28, 38, 38, 38, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342002224 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 Building ZINC000342002224 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342002224 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 701) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342002224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342002224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342002224 none CC[C@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 4, 13, 13, 30, 44, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 18, 18, 30, 30, 44, 44, 44, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 702) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342002224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342002224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342002224 none CC[C@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [16, 12, 4, 12, 12, 28, 38, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 19, 19, 19, 28, 28, 38, 38, 38, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342002224 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342002224 Building ZINC000342003167 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342003167 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/703 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342003167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342003167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342003167 none CC[C@@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [16, 12, 4, 12, 12, 28, 39, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 19, 19, 19, 28, 28, 39, 39, 39, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/704 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342003167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342003167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342003167 none CC[C@@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [14, 12, 4, 12, 12, 29, 43, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 29, 29, 43, 43, 43, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342003167 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 Building ZINC000342003167 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342003167 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 703) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342003167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342003167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342003167 none CC[C@@H](CSC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [16, 12, 4, 12, 12, 28, 39, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 19, 19, 19, 28, 28, 39, 39, 39, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 704) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342003167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342003167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342003167 none CC[C@@H](CSC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.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'] dock atom type numbers: [5, 5, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [14, 12, 4, 12, 12, 29, 43, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 29, 29, 43, 43, 43, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342003167 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342003167 Building ZINC000342028229 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028229 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/705 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028229 none CO[C@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 31, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 20, 20, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/706 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028229 none CO[C@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 31, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028229 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 Building ZINC000342028229 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028229 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 705) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028229 none CO[C@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 31, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 20, 20, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 706) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028229 none CO[C@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 31, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028229 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028229 Building ZINC000342028231 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028231 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/707 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028231 none CO[C@@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 30, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/708 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028231 none CO[C@@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 30, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028231 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 Building ZINC000342028231 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028231 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 707) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028231 none CO[C@@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 30, 45, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 18, 18, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 708) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028231 none CO[C@@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 30, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028231 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028231 Building ZINC000342028233 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028233 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/709 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028233 none CO[C@@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 31, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/710 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028233 none CO[C@@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 31, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028233 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 Building ZINC000342028233 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028233 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 709) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028233 none CO[C@@H]1CCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 31, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 710) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028233 none CO[C@@H]1CCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 31, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028233 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028233 Building ZINC000342028234 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028234 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/711 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028234 none CO[C@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 30, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/712 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028234 none CO[C@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 31, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028234 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 Building ZINC000342028234 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028234 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 711) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028234 none CO[C@H]1CCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 30, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 712) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CO[C@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342028234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000342028234 none CO[C@H]1CCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 5, 7, 5, 5, 5, 5, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 31, 49, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028234 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028234 Building ZINC000342028828 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028828 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/713 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028828 none C[C@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 20, 24, 24, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 7, 7, 7, 22, 22, 24, 22, 24, 24, 48, 24, 24, 3, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/714 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028828 none C[C@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 22, 25, 25, 25, 25, 25, 25, 25, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 24, 24, 24, 25, 25, 25, 50, 25, 25, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028828 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 Building ZINC000342028828 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028828 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 713) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028828 none C[C@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 7, 20, 24, 24, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 7, 7, 7, 22, 22, 24, 22, 24, 24, 48, 24, 24, 3, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 714) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028828 none C[C@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 8, 8, 22, 25, 25, 25, 25, 25, 25, 25, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 24, 24, 24, 25, 25, 25, 50, 25, 25, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028828 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028828 Building ZINC000342028830 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028830 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/715 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028830 none C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 10, 10, 10, 27, 27, 27, 27, 27, 27, 54, 27, 27, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/716 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028830 none C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 22, 23, 23, 22, 23, 23, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 10, 10, 10, 22, 22, 22, 22, 23, 23, 46, 23, 23, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028830 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 Building ZINC000342028830 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342028830 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 715) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342028830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028830 none C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 27, 27, 27, 27, 27, 27, 27, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 10, 10, 10, 27, 27, 27, 27, 27, 27, 54, 27, 27, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 716) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342028830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342028830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342028830 none C[C@@H](CCc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 22, 23, 23, 22, 23, 23, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 10, 10, 10, 22, 22, 22, 22, 23, 23, 46, 23, 23, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342028830 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342028830 Building ZINC000186413436 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186413436 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/717 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186413436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186413436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000186413436 none CCCN(CC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 12, 12, 18, 18, 18, 18, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 8, 8, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/718 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186413436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186413436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000186413436 none CCCN(CC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 14, 14, 17, 18, 18, 18, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 9, 9, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186413436 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 Building ZINC000186413436 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186413436 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 717) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186413436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186413436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000186413436 none CCCN(CC(=O)OC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 12, 12, 18, 18, 18, 18, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 8, 8, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 718) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000186413436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186413436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000186413436 none CCCN(CC(=O)OC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 14, 14, 17, 18, 18, 18, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 9, 9, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186413436 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186413436 Building ZINC000286258059 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286258059 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/719 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286258059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258059 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 4, 4, 4, 10, 10, 10, 4, 4, 13, 13, 13, 13, 13, 13, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/720 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286258059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258059 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 6, 6, 6, 11, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 30, 30, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000286258059 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 Building ZINC000286258059 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286258059 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 719) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286258059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258059 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 4, 4, 4, 10, 10, 10, 4, 4, 13, 13, 13, 13, 13, 13, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 720) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286258059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258059 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 6, 6, 6, 11, 11, 11, 6, 6, 7, 7, 7, 7, 7, 7, 30, 30, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000286258059 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258059 Building ZINC000286258068 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286258068 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/721 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286258068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258068 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 6, 6, 6, 6, 29, 29, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/722 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286258068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258068 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 4, 4, 4, 9, 9, 9, 4, 4, 11, 11, 11, 11, 11, 11, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000286258068 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 Building ZINC000286258068 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000286258068 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 721) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000286258068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258068 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 6, 6, 6, 6, 29, 29, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 722) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl) `ZINC000286258068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000286258068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000286258068 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccn[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 8, 8, 6, 1, 1, 16, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 4, 4, 4, 9, 9, 9, 4, 4, 11, 11, 11, 11, 11, 11, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000286258068 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000286258068 Building ZINC000342059264 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342059264 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/723 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1) `ZINC000342059264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342059264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342059264 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.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, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 14, 14, 9, 9, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 4, 21, 21, 21, 9] 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/724 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1) `ZINC000342059264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342059264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342059264 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.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, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 19, 19, 19, 9] 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342059264 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 Building ZINC000342059264 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342059264 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 723) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1) `ZINC000342059264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342059264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342059264 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.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, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 14, 14, 9, 9, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 4, 21, 21, 21, 9] 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 724) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1) `ZINC000342059264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342059264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342059264 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.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, 5, 15, 15, 15, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 4, 19, 19, 19, 9] 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342059264 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342059264 Building ZINC000342070631 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342070631 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/725 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(O)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342070631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070631 none C[C@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 13, 13, 24, 27, 27, 24, 27, 27, 27, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 13, 13, 13, 24, 24, 27, 27, 54, 27, 27, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/726 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(O)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342070631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070631 none C[C@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 13, 13, 22, 24, 24, 22, 24, 24, 24, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 22, 22, 24, 24, 48, 24, 24, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342070631 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 Building ZINC000342070631 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342070631 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 725) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(O)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342070631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070631 none C[C@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 13, 13, 24, 27, 27, 24, 27, 27, 27, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 13, 13, 13, 24, 24, 27, 27, 54, 27, 27, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 726) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1ccc(O)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342070631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070631 none C[C@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 13, 13, 22, 24, 24, 22, 24, 24, 24, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 22, 22, 24, 24, 48, 24, 24, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342070631 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070631 Building ZINC000342070632 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342070632 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/727 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(O)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342070632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070632 none C[C@@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 22, 25, 25, 22, 25, 25, 25, 3, 6, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 15, 15, 15, 22, 22, 25, 25, 50, 25, 25, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/728 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1ccc(O)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342070632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070632 none C[C@@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 12, 12, 22, 23, 23, 22, 23, 23, 23, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 12, 12, 12, 22, 22, 23, 23, 46, 23, 23, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342070632 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 Building ZINC000342070632 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342070632 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 727) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](Cc1ccc(O)cc1)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342070632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070632 none C[C@@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 22, 25, 25, 22, 25, 25, 25, 3, 6, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 15, 15, 15, 22, 22, 25, 25, 50, 25, 25, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 728) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](Cc1ccc(O)cc1)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342070632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342070632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000342070632 none C[C@@H](Cc1ccc(O)cc1)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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 12, 12, 22, 23, 23, 22, 23, 23, 23, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 12, 12, 12, 22, 22, 23, 23, 46, 23, 23, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342070632 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342070632 Building ZINC000342076789 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342076789 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/729 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)cn1) `ZINC000342076789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342076789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342076789 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)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', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 16, 1, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 9, 9, 9, 9, 6, 6, 15, 15, 15, 15, 15, 6, 3, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/730 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)cn1) `ZINC000342076789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342076789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342076789 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)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', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 16, 1, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 4, 3, 9, 9, 9, 9, 6, 6, 16, 16, 16, 16, 16, 6, 3, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342076789 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 Building ZINC000342076789 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342076789 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 729) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)cn1) `ZINC000342076789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342076789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342076789 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)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', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 16, 1, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 9, 9, 9, 9, 6, 6, 15, 15, 15, 15, 15, 6, 3, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 730) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)cn1) `ZINC000342076789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342076789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000342076789 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cc(Cl)c(C)c2F)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', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 16, 1, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 4, 3, 9, 9, 9, 9, 6, 6, 16, 16, 16, 16, 16, 6, 3, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342076789 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342076789 Building ZINC000342104968 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342104968 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/731 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342104968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104968 none COc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 6, 25, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 40, 40, 40, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/732 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342104968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104968 none COc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 6, 28, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 28, 28, 28, 42, 42, 42, 28, 28, 28, 6, 6, 6, 6, 6, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342104968 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 Building ZINC000342104968 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342104968 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 731) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342104968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104968 none COc1ccc2c(c1)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 6, 25, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 40, 40, 40, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 732) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342104968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104968 none COc1ccc2c(c1)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 6, 28, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 28, 28, 28, 42, 42, 42, 28, 28, 28, 6, 6, 6, 6, 6, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342104968 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104968 Building ZINC000342104969 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342104969 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/733 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342104969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104969 none COc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 6, 28, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 28, 28, 28, 42, 42, 42, 28, 28, 28, 6, 6, 6, 6, 6, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/734 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342104969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104969 none COc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 6, 25, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 41, 41, 41, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342104969 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 Building ZINC000342104969 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342104969 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 733) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342104969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104969 none COc1ccc2c(c1)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 6, 28, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 28, 28, 28, 42, 42, 42, 28, 28, 28, 6, 6, 6, 6, 6, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 734) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2) `ZINC000342104969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342104969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342104969 none COc1ccc2c(c1)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 6, 25, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 25, 25, 41, 41, 41, 25, 25, 25, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342104969 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342104969 Building ZINC000342118638 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118638 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/735 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118638 none C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 78, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 6, 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, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/736 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118638 none C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 16, 14, 1, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 81, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118638 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 Building ZINC000342118638 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118638 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 735) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118638 none C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 78, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 6, 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, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 736) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118638 none C[C@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 16, 14, 1, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 81, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118638 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118638 Building ZINC000342118639 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118639 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/737 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118639 none C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 12, 1, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 87, 26, 26, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 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, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/738 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118639 none C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 78, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 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, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118639 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 Building ZINC000342118639 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118639 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 737) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118639 none C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 26, 29, 29, 15, 15, 15, 15, 15, 15, 15, 15, 12, 1, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 87, 26, 26, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 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, 47, 48, 49, 50]) total number of confs: 192 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 738) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118639 none C[C@@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 78, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 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, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118639 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118639 Building ZINC000342118640 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118640 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/739 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118640 none C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 24, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 75, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 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, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/740 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118640 none C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 16, 16, 16, 16, 16, 16, 16, 16, 14, 1, 14, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 75, 25, 25, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118640 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 Building ZINC000342118640 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118640 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 739) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118640 none C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 24, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 75, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 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, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 740) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118640 none C[C@H](O)C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 16, 16, 16, 16, 16, 16, 16, 16, 14, 1, 14, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 25, 25, 25, 75, 25, 25, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118640 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118640 Building ZINC000342118641 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118641 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/741 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118641 none C[C@@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 14, 1, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 75, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/742 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118641 none C[C@@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 15, 1, 14, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 28, 28, 28, 84, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118641 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 Building ZINC000342118641 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342118641 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 741) grep: /scratch/xiaobo/25650/xaq-8058115.17/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](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342118641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118641 none C[C@@H](O)C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 14, 1, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 75, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 742) grep: /scratch/xiaobo/25650/xaq-8058115.17/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](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342118641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342118641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000342118641 none C[C@@H](O)C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 15, 1, 14, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 28, 28, 28, 84, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342118641 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342118641 Building ZINC000342170926 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342170926 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/743 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342170926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342170926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342170926 none CSCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.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'] dock atom type numbers: [5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 15, 5, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 26, 25, 20, 20, 15, 15, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/744 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342170926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342170926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342170926 none CSCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.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'] dock atom type numbers: [5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 15, 5, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 25, 26, 20, 20, 15, 15, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342170926 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 Building ZINC000342170926 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342170926 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 743) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CSCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342170926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342170926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342170926 none CSCCCN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.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'] dock atom type numbers: [5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 15, 5, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 26, 25, 20, 20, 15, 15, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 744) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CSCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000342170926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342170926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342170926 none CSCCCN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.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'] dock atom type numbers: [5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 15, 5, 2, 5, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 25, 26, 20, 20, 15, 15, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342170926 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342170926 Building ZINC000190969727 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190969727 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/745 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(F)F)cc1) `ZINC000190969727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190969727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190969727 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 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: [5, 2, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 23, 29, 29, 29, 29, 29, 29, 41, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 23, 23, 29, 29, 29, 29, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/746 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(F)F)cc1) `ZINC000190969727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190969727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190969727 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 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: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 21, 29, 29, 29, 29, 29, 29, 41, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 21, 21, 29, 29, 29, 29, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190969727 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 Building ZINC000190969727 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190969727 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 745) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(F)F)cc1) `ZINC000190969727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190969727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190969727 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 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: [5, 2, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 23, 29, 29, 29, 29, 29, 29, 41, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 23, 23, 29, 29, 29, 29, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 746) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(F)F)cc1) `ZINC000190969727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190969727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000190969727 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccccc2OC(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 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: [5, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 21, 29, 29, 29, 29, 29, 29, 41, 48, 48, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 21, 21, 29, 29, 29, 29, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000190969727 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000190969727 Building ZINC000342186612 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342186612 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/747 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/747' -> `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)CCCO1) `ZINC000342186612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342186612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186612 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens 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, 32, 32, 32, 32, 20, 2, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 45, 45, 45, 45, 45, 32, 32, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/748 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/748' -> `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)CCCO1) `ZINC000342186612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342186612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186612 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 34, 34, 34, 22, 2, 23, 1, 1, 1, 3, 3, 1, 3, 3, 3, 34, 34, 34, 34, 48, 48, 48, 48, 48, 34, 34, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342186612 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 Building ZINC000342186612 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342186612 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 747) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1) `ZINC000342186612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342186612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186612 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens 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, 32, 32, 32, 32, 20, 2, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 45, 45, 45, 45, 45, 32, 32, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 748) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1) `ZINC000342186612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342186612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186612 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 34, 34, 34, 22, 2, 23, 1, 1, 1, 3, 3, 1, 3, 3, 3, 34, 34, 34, 34, 48, 48, 48, 48, 48, 34, 34, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342186612 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186612 Building ZINC000342186613 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342186613 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/749 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/749' -> `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)CCCO1) `ZINC000342186613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342186613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186613 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens 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, 33, 33, 33, 33, 25, 1, 25, 1, 1, 1, 3, 3, 1, 3, 3, 3, 33, 33, 33, 33, 48, 48, 48, 48, 48, 33, 33, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33] 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: 163 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/750 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/750' -> `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)CCCO1) `ZINC000342186613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342186613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186613 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens 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, 31, 31, 31, 31, 21, 1, 21, 1, 1, 1, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 47, 47, 47, 47, 47, 31, 31, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31] 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: 154 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342186613 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 Building ZINC000342186613 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342186613 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 749) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1) `ZINC000342186613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342186613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186613 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens 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, 33, 33, 33, 33, 25, 1, 25, 1, 1, 1, 3, 3, 1, 3, 3, 3, 33, 33, 33, 33, 48, 48, 48, 48, 48, 33, 33, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33] 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: 163 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 750) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1) `ZINC000342186613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342186613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000342186613 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCCO1 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', '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, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 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] 0 hydrogens 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, 31, 31, 31, 31, 21, 1, 21, 1, 1, 1, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 47, 47, 47, 47, 47, 31, 31, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31] 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: 154 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342186613 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342186613 Building ZINC000342190687 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342190687 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/751 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000342190687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342190687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342190687 none COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['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', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 23, 23, 23, 23, 23, 10, 1, 12, 1, 1, 1, 5, 5, 2, 5, 5, 5, 23, 23, 43, 43, 43, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 23, 23, 23, 23] 47 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/752 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000342190687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342190687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342190687 none COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['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', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 21, 21, 21, 21, 8, 1, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 21, 21, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 21, 21, 21, 21] 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: 75 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342190687 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 Building ZINC000342190687 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342190687 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 751) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000342190687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342190687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342190687 none COC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['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', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 23, 23, 23, 23, 23, 10, 1, 12, 1, 1, 1, 5, 5, 2, 5, 5, 5, 23, 23, 43, 43, 43, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 23, 23, 23, 23] 47 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 752) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000342190687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342190687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000342190687 none COC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['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', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 21, 21, 21, 21, 8, 1, 9, 1, 1, 1, 5, 5, 1, 1, 5, 5, 21, 21, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 21, 21, 21, 21] 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: 75 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342190687 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342190687 Building ZINC000342201822 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342201822 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/753 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000342201822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342201822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000342201822 none CC(C)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 12, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 8, 8, 30, 30, 30, 30, 30, 30, 30, 21, 21, 8, 8, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 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, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/754 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000342201822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342201822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000342201822 none CC(C)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 31, 13, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 8, 8, 31, 31, 31, 31, 31, 31, 31, 24, 24, 8, 8, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 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/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342201822 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 Building ZINC000342201822 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342201822 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 753) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000342201822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342201822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000342201822 none CC(C)COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 12, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 8, 8, 30, 30, 30, 30, 30, 30, 30, 21, 21, 8, 8, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 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, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 754) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1) `ZINC000342201822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342201822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000342201822 none CC(C)COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 31, 13, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 8, 8, 31, 31, 31, 31, 31, 31, 31, 24, 24, 8, 8, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 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/25650/xaq-8058115.17/working/building/ZINC000342201822 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342201822 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342201822 Building ZINC000186693782 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186693782 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/755 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000186693782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186693782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000186693782 none CC(C)(O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 21, 29, 29, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 87, 29, 29, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/756 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000186693782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186693782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000186693782 none CC(C)(O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 21, 29, 29, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 87, 29, 29, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186693782 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 Building ZINC000186693782 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186693782 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 755) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000186693782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186693782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000186693782 none CC(C)(O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 21, 29, 29, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 87, 29, 29, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 756) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC000186693782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186693782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000186693782 none CC(C)(O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 21, 29, 29, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 87, 29, 29, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000186693782 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000186693782 Building ZINC000342267296 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342267296 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/757 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342267296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267296 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 28, 28, 21, 21, 21, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 28, 28, 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, 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/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/758 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342267296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267296 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 28, 28, 23, 23, 23, 10, 10, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 28, 28, 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, 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/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342267296 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 Building ZINC000342267296 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342267296 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 757) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342267296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267296 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 28, 28, 21, 21, 21, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 28, 28, 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, 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/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 758) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342267296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267296 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 28, 28, 23, 23, 23, 10, 10, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 28, 28, 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, 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/25650/xaq-8058115.17/working/building/ZINC000342267296 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342267296 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267296 Building ZINC000342267297 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342267297 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/759 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342267297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267297 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 28, 28, 24, 24, 24, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/760 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342267297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267297 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 28, 28, 21, 21, 21, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342267297 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 Building ZINC000342267297 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342267297 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 759) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342267297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267297 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 28, 28, 24, 24, 24, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 760) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1) `ZINC000342267297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342267297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267297 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 28, 28, 21, 21, 21, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342267297 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267297 Building ZINC000342267301 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342267301 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/761 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1) `ZINC000342267301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342267301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267301 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 28, 28, 25, 25, 25, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/762 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1) `ZINC000342267301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342267301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267301 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 29, 29, 25, 25, 25, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342267301 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 Building ZINC000342267301 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342267301 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 761) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1) `ZINC000342267301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342267301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267301 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 28, 28, 25, 25, 25, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 28, 28, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 762) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1) `ZINC000342267301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342267301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342267301 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCO[C@@H]1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 29, 29, 25, 25, 25, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342267301 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342267301 Building ZINC000342285900 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342285900 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/763 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCN1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342285900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342285900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342285900 none CCCN(CCN1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 2, 4, 8, 12, 19, 19, 19, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/764 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCN1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342285900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342285900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342285900 none CCCN(CCN1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 2, 4, 8, 11, 19, 19, 19, 18, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 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, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342285900 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 Building ZINC000342285900 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342285900 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 763) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCN1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342285900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342285900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342285900 none CCCN(CCN1CCCC1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 2, 4, 8, 12, 19, 19, 19, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 91 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 764) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCN1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000342285900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342285900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342285900 none CCCN(CCN1CCCC1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 2, 4, 8, 11, 19, 19, 19, 18, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 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, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342285900 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342285900 Building ZINC000342287666 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342287666 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/765 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000342287666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342287666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000342287666 none COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 17, 17, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 17, 17, 17, 25, 25, 25, 17, 17, 3, 3, 3, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/766 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000342287666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342287666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000342287666 none COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 18, 18, 18, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 18, 18, 18, 26, 26, 26, 18, 18, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342287666 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 Building ZINC000342287666 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342287666 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 765) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000342287666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342287666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000342287666 none COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 17, 17, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 17, 17, 17, 25, 25, 25, 17, 17, 3, 3, 3, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 766) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000342287666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342287666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000342287666 none COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 18, 18, 18, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 18, 18, 18, 26, 26, 26, 18, 18, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342287666 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342287666 Building ZINC000342360369 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342360369 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/767 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(F)c(F)c1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342360369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342360369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342360369 none O=C(NCCc1ccc(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.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/768 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(F)c(F)c1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342360369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342360369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342360369 none O=C(NCCc1ccc(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.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342360369 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 Building ZINC000342360369 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342360369 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 767) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCc1ccc(F)c(F)c1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342360369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342360369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342360369 none O=C(NCCc1ccc(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.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 768) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCc1ccc(F)c(F)c1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342360369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342360369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342360369 none O=C(NCCc1ccc(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.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 31, 31, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342360369 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342360369 Building ZINC000342364207 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342364207 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/769 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(nc(C)c2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)s1) `ZINC000342364207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342364207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342364207 none Cc1cn2c(nc(C)c2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', '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', 'S.3', '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, 8, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 50, 50, 50, 30, 9, 4, 9, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/770 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(nc(C)c2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)s1) `ZINC000342364207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342364207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342364207 none Cc1cn2c(nc(C)c2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', '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', 'S.3', '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, 8, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 50, 50, 50, 29, 8, 4, 8, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 8, 8, 8, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342364207 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 Building ZINC000342364207 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342364207 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 769) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cn2c(nc(C)c2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)s1) `ZINC000342364207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342364207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342364207 none Cc1cn2c(nc(C)c2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', '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', 'S.3', '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, 8, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 50, 50, 50, 30, 9, 4, 9, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 770) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cn2c(nc(C)c2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)s1) `ZINC000342364207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342364207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000342364207 none Cc1cn2c(nc(C)c2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', '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', 'S.3', '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, 8, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 50, 50, 50, 29, 8, 4, 8, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 8, 8, 8, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342364207 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342364207 Building ZINC000342388864 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342388864 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/771 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1) `ZINC000342388864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342388864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342388864 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 12, 28, 28, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 11, 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, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/772 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1) `ZINC000342388864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342388864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342388864 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 29, 29, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 11, 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, 39]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342388864 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 Building ZINC000342388864 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342388864 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 771) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1) `ZINC000342388864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342388864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342388864 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 12, 28, 28, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 11, 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, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 772) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1) `ZINC000342388864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342388864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000342388864 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3cccc(Cl)c3[nH]2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 29, 29, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 11, 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, 39]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342388864 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342388864 Building ZINC000342444255 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342444255 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/773 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/773' -> `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(F)cc1) `ZINC000342444255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342444255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000342444255 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 32, 32, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/774 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/774' -> `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(F)cc1) `ZINC000342444255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342444255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000342444255 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 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, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342444255 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 Building ZINC000342444255 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342444255 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 773) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342444255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342444255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000342444255 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 17, 17, 32, 32, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 774) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342444255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342444255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000342444255 none O=C(NCCc1c[nH]c2ccc(F)cc12)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 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, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342444255 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342444255 Building ZINC000342548875 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342548875 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/775 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342548875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548875 none O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/776 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342548875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548875 none O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342548875 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 Building ZINC000342548875 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342548875 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 775) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342548875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548875 none O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 776) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342548875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548875 none O=C(N[C@@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342548875 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548875 Building ZINC000342548876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342548876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/777 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342548876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548876 none O=C(N[C@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/778 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342548876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548876 none O=C(N[C@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342548876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 Building ZINC000342548876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342548876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 777) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342548876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548876 none O=C(N[C@H]1COc2ccc(F)cc2C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 778) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000342548876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342548876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000342548876 none O=C(N[C@H]1COc2ccc(F)cc2C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342548876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342548876 Building ZINC000342596310 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596310 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/779 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/780 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/781 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/781' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/782 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/782' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596310 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 Building ZINC000342596310 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596310 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 779) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 780) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 781) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 782) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596310 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 Building ZINC000342596310 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596310 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 779) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 780) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 781) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 782) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596310 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 Building ZINC000342596310 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596310 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 779) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 780) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 9, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 26, 26, 45, 50, 50, 45, 50, 50, 26, 26, 26, 4, 3, 3, 3, 3, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 781) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 782) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596310 none C[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 43, 50, 50, 43, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 43, 43, 50, 50, 43, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596310 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596310 Building ZINC000342596311 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596311 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/783 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/784 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/785 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/785' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/786 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/786' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596311 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 Building ZINC000342596311 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596311 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 783) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 784) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 785) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 786) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596311 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 Building ZINC000342596311 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596311 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 783) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 784) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 785) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 786) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596311 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 Building ZINC000342596311 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596311 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 783) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 784) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 44, 50, 50, 49, 50, 50, 28, 28, 28, 4, 3, 3, 3, 3, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 785) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 786) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596311 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 45, 50, 50, 50, 50, 50, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27, 27, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596311 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596311 Building ZINC000342596312 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596312 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/787 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/788 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/789 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/789' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/790 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/790' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596312 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 Building ZINC000342596312 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596312 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 787) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 788) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 789) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 790) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596312 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 Building ZINC000342596312 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596312 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 787) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 788) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 789) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 790) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596312 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 Building ZINC000342596312 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596312 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 787) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 788) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 46, 50, 50, 46, 50, 50, 31, 31, 31, 2, 3, 3, 3, 3, 31, 31, 31, 31, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 789) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 790) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596312.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596312 none C[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 45, 50, 50, 46, 50, 50, 33, 33, 33, 3, 3, 3, 3, 3, 33, 33, 33, 33, 45, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596312 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596312 Building ZINC000342596313 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596313 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/791 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/792 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/793 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/793' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/794 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/794' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596313 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 Building ZINC000342596313 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596313 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 791) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 792) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 793) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 794) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596313 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 Building ZINC000342596313 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596313 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 791) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 792) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 793) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 794) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596313 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 Building ZINC000342596313 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342596313 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 791) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 792) grep: /scratch/xiaobo/25650/xaq-8058115.17/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]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 34, 34, 45, 50, 50, 45, 50, 50, 34, 34, 34, 4, 3, 3, 3, 3, 34, 34, 34, 34, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 793) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 794) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1) `ZINC000342596313.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342596313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000342596313 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 30, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 45, 50, 50, 45, 50, 50, 30, 30, 30, 2, 3, 3, 3, 3, 30, 30, 30, 30, 45, 45, 50, 50, 45, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342596313 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342596313 Building ZINC000342618408 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342618408 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/795 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/796 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/797 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/797' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/798 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/798' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342618408 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 Building ZINC000342618408 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342618408 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 795) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 796) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 797) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 798) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342618408 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 Building ZINC000342618408 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342618408 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 795) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 796) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 797) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 798) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342618408 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 Building ZINC000342618408 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342618408 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 795) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 796) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 35, 38, 38, 47, 50, 50, 47, 50, 50, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 35, 35, 38, 38, 38, 47, 47, 50, 50, 47, 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, 39, 40, 41, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 797) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 798) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342618408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342618408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000342618408 none C[C@H](CN(C)Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 3, 10, 10, 26, 32, 32, 48, 50, 50, 48, 50, 50, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 26, 26, 32, 32, 32, 48, 48, 50, 50, 48, 50, 50, 3, 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: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342618408 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342618408 Building ZINC000342628273 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628273 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/799 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628273 none CCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 23, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/800 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628273 none CCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 23, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628273 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 Building ZINC000342628273 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628273 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 799) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628273 none CCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 23, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 800) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628273 none CCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 23, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628273 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628273 Building ZINC000342628285 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628285 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/801 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628285 none CCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 3, 6, 6, 23, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/802 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628285 none CCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 23, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628285 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 Building ZINC000342628285 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628285 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 801) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628285 none CCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 3, 6, 6, 23, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 802) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000342628285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342628285 none CCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 23, 11, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 23, 23, 23, 23, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628285 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628285 Building ZINC000342628876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/803 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/803' -> `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]2CCOc3ccccc32)cn1) `ZINC000342628876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628876 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/804 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/804' -> `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]2CCOc3ccccc32)cn1) `ZINC000342628876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628876 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 Building ZINC000342628876 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628876 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 803) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cn1) `ZINC000342628876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628876 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 804) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cn1) `ZINC000342628876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628876 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628876 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628876 Building ZINC000342628877 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628877 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/805 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/805' -> `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]2CCOc3ccccc32)cn1) `ZINC000342628877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628877 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/806 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/806' -> `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]2CCOc3ccccc32)cn1) `ZINC000342628877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628877 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628877 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 Building ZINC000342628877 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342628877 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 805) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cn1) `ZINC000342628877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342628877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628877 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 806) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cn1) `ZINC000342628877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342628877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342628877 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCOc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 46, 47]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342628877 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342628877 Building ZINC000342651323 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342651323 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/807 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1) `ZINC000342651323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342651323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651323 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 31, 31, 31, 33, 33, 12, 12, 12, 12, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/808 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1) `ZINC000342651323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342651323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651323 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 27, 27, 27, 30, 30, 11, 11, 11, 11, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 27, 27, 27, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342651323 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 Building ZINC000342651323 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342651323 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 807) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1) `ZINC000342651323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342651323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651323 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 31, 31, 31, 33, 33, 12, 12, 12, 12, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 31, 31, 31, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 808) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1) `ZINC000342651323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342651323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651323 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 27, 27, 27, 30, 30, 11, 11, 11, 11, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 27, 27, 27, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342651323 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651323 Building ZINC000342651326 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342651326 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/809 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1) `ZINC000342651326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342651326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651326 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 22, 22, 22, 35, 35, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/810 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1) `ZINC000342651326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342651326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651326 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 29, 29, 29, 36, 36, 12, 12, 12, 12, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342651326 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 Building ZINC000342651326 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342651326 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 809) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1) `ZINC000342651326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342651326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651326 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 22, 22, 22, 35, 35, 11, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 810) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1) `ZINC000342651326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342651326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000342651326 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)nn1[C@@H](C)C1CC1 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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 29, 29, 29, 36, 36, 12, 12, 12, 12, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342651326 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342651326 Building ZINC000342660548 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342660548 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/811 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1) `ZINC000342660548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342660548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660548 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 40, 40, 40, 46, 46, 17, 17, 17, 17, 8, 4, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 161 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/812 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1) `ZINC000342660548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342660548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660548 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 39, 39, 39, 48, 48, 14, 14, 14, 14, 6, 4, 4, 4, 4, 4, 4, 39, 39, 39, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342660548 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 Building ZINC000342660548 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342660548 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 811) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1) `ZINC000342660548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342660548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660548 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 40, 40, 40, 46, 46, 17, 17, 17, 17, 8, 4, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 161 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 812) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1) `ZINC000342660548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342660548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660548 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 39, 39, 39, 48, 48, 14, 14, 14, 14, 6, 4, 4, 4, 4, 4, 4, 39, 39, 39, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342660548 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660548 Building ZINC000342660571 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342660571 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/813 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1) `ZINC000342660571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342660571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660571 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 38, 38, 38, 49, 49, 16, 16, 16, 16, 7, 4, 4, 4, 4, 4, 4, 38, 38, 38, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/814 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1) `ZINC000342660571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342660571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660571 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 39, 39, 39, 46, 46, 16, 16, 16, 16, 8, 4, 4, 4, 4, 4, 4, 39, 39, 39, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 164 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342660571 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 Building ZINC000342660571 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342660571 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 813) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1) `ZINC000342660571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342660571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660571 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 38, 38, 38, 49, 49, 16, 16, 16, 16, 7, 4, 4, 4, 4, 4, 4, 38, 38, 38, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 814) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1) `ZINC000342660571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342660571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342660571 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)nn1[C@@H](C)C1CC1 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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 39, 39, 39, 46, 46, 16, 16, 16, 16, 8, 4, 4, 4, 4, 4, 4, 39, 39, 39, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 164 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342660571 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342660571 Building ZINC000342768058 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768058 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/815 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/816 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/817 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/817' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/818 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/818' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768058 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 Building ZINC000342768058 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768058 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 815) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 816) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 817) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 818) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768058 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 Building ZINC000342768058 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768058 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 815) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 816) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 817) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 818) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768058 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 Building ZINC000342768058 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768058 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 815) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 816) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(N[C@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 817) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 818) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768058.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768058 none O=C(N[C@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 21, 21, 21, 21, 21, 21, 50, 50, 21, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 21, 21, 50, 50, 48, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768058 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768058 Building ZINC000342768059 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768059 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/819 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/820 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/821 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/821' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/822 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/822' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768059 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 Building ZINC000342768059 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768059 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 819) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 820) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 821) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 822) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768059 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 Building ZINC000342768059 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768059 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 819) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 820) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 821) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 822) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768059 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 Building ZINC000342768059 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342768059 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 819) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 820) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccccc2F)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 20, 20, 20, 50, 50, 20, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 20, 20, 20, 20, 50, 50, 48, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 821) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 822) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(c2ccccc2F)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000342768059.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342768059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000342768059 none O=C(N[C@@H]1CCCN(c2ccccc2F)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 18, 18, 18, 50, 50, 46, 50, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342768059 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342768059 Building ZINC000342773597 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342773597 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/823 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCN1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342773597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342773597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000342773597 none CCCN(CCN1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 7, 11, 18, 18, 18, 18, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 11, 11, 11, 11, 11, 8, 8, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/824 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCN1CCCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342773597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342773597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000342773597 none CCCN(CCN1CCCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 7, 11, 18, 18, 18, 18, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 11, 11, 11, 11, 11, 8, 8, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342773597 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 Building ZINC000342773597 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342773597 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 823) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCN1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342773597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342773597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000342773597 none CCCN(CCN1CCCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 7, 11, 18, 18, 18, 18, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 11, 11, 11, 11, 11, 8, 8, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 824) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCN(CCN1CCCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000342773597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342773597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000342773597 none CCCN(CCN1CCCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 7, 11, 18, 18, 18, 18, 18, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 11, 11, 11, 11, 11, 8, 8, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342773597 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773597 Building ZINC000342773818 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342773818 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/825 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342773818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773818 none CC[C@@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 34, 34, 34, 16, 28, 28, 16, 28, 28, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 34, 34, 34, 28, 28, 16, 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, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/826 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342773818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773818 none CC[C@@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [22, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 35, 35, 35, 16, 29, 29, 16, 29, 29, 22, 22, 22, 22, 22, 6, 5, 5, 5, 5, 35, 35, 35, 29, 29, 16, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342773818 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 Building ZINC000342773818 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342773818 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 825) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342773818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773818 none CC[C@@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 34, 34, 34, 16, 28, 28, 16, 28, 28, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 34, 34, 34, 28, 28, 16, 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, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 826) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342773818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773818 none CC[C@@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [22, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 35, 35, 35, 16, 29, 29, 16, 29, 29, 22, 22, 22, 22, 22, 6, 5, 5, 5, 5, 35, 35, 35, 29, 29, 16, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342773818 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773818 Building ZINC000342773819 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342773819 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/827 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342773819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773819 none CC[C@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [22, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 36, 36, 36, 16, 29, 29, 26, 29, 29, 22, 22, 22, 22, 22, 6, 5, 5, 5, 5, 36, 36, 36, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/828 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342773819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773819 none CC[C@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 33, 33, 33, 16, 27, 27, 25, 27, 27, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 33, 33, 33, 27, 27, 25, 27, 27] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342773819 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 Building ZINC000342773819 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342773819 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 827) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342773819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773819 none CC[C@](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [22, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 36, 36, 36, 16, 29, 29, 26, 29, 29, 22, 22, 22, 22, 22, 6, 5, 5, 5, 5, 36, 36, 36, 29, 29, 26, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 828) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1) `ZINC000342773819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342773819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342773819 none CC[C@](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)(C(=O)OC)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 12, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 16, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 16, 33, 33, 33, 16, 27, 27, 25, 27, 27, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 33, 33, 33, 27, 27, 25, 27, 27] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342773819 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342773819 Building ZINC000191089938 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191089938 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/829 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(C)(C)C2)cc1) `ZINC000191089938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191089938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191089938 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/830 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(C)(C)C2)cc1) `ZINC000191089938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191089938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191089938 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191089938 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 Building ZINC000191089938 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191089938 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 829) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(C)(C)C2)cc1) `ZINC000191089938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191089938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191089938 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 830) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(C)(C)C2)cc1) `ZINC000191089938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191089938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191089938 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCCC3)OC(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.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191089938 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191089938 Building ZINC000342807258 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342807258 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/831 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/832 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/833 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/833' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/834 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/834' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342807258 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 Building ZINC000342807258 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342807258 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 831) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 832) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 833) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 834) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342807258 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 Building ZINC000342807258 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342807258 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 831) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 832) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 833) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 834) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342807258 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 Building ZINC000342807258 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000342807258 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 831) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 832) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 28, 28, 28, 28, 28, 15, 15, 15, 12, 12, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 833) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 834) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c1ccc2c(c1)CCC2)C1CCCCC1) `ZINC000342807258.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000342807258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000342807258 none CN(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 27, 27, 27, 27, 27, 15, 15, 15, 13, 13, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342807258 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342807258 Building ZINC000187391825 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187391825 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/835 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C) `ZINC000187391825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187391825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000187391825 none Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/836 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C) `ZINC000187391825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187391825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000187391825 none Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 15, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187391825 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 Building ZINC000187391825 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187391825 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 835) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C) `ZINC000187391825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187391825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000187391825 none Cc1ccc2c(c1)nc(CNC(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 836) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C) `ZINC000187391825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187391825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000187391825 none Cc1ccc2c(c1)nc(CNC(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 15, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187391825 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187391825 Building ZINC000342883614 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342883614 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/837 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/837' -> `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](Nc3ccccc3)C2)cn1) `ZINC000342883614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342883614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883614 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 20, 34, 34, 22, 34, 34, 6, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 20, 34, 34, 22, 34, 34, 6, 6, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/838 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/838' -> `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](Nc3ccccc3)C2)cn1) `ZINC000342883614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342883614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883614 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 20, 34, 34, 20, 34, 34, 5, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 5, 5, 5, 5, 20, 34, 34, 20, 34, 34, 5, 5, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342883614 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 Building ZINC000342883614 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342883614 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 837) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Nc3ccccc3)C2)cn1) `ZINC000342883614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342883614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883614 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 20, 34, 34, 22, 34, 34, 6, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6, 6, 6, 6, 20, 34, 34, 22, 34, 34, 6, 6, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 838) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Nc3ccccc3)C2)cn1) `ZINC000342883614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342883614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883614 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 20, 34, 34, 20, 34, 34, 5, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 5, 5, 5, 5, 20, 34, 34, 20, 34, 34, 5, 5, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342883614 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883614 Building ZINC000342883615 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342883615 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/839 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/839' -> `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](Nc3ccccc3)C2)cn1) `ZINC000342883615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342883615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883615 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 24, 33, 33, 27, 33, 33, 6, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 6, 24, 33, 33, 29, 33, 33, 6, 6, 3] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/840 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/840' -> `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](Nc3ccccc3)C2)cn1) `ZINC000342883615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342883615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883615 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 6, 6, 6, 20, 38, 38, 26, 38, 38, 6, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 20, 38, 38, 28, 38, 38, 6, 6, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342883615 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 Building ZINC000342883615 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342883615 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 839) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Nc3ccccc3)C2)cn1) `ZINC000342883615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342883615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883615 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 24, 33, 33, 27, 33, 33, 6, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 6, 24, 33, 33, 29, 33, 33, 6, 6, 3] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 840) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Nc3ccccc3)C2)cn1) `ZINC000342883615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342883615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000342883615 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Nc3ccccc3)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 6, 6, 6, 20, 38, 38, 26, 38, 38, 6, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 20, 38, 38, 28, 38, 38, 6, 6, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342883615 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342883615 Building ZINC000187504352 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187504352 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/841 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@](O)(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC000187504352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187504352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000187504352 none C[C@@](O)(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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] 1 hydrogens 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, 16, 27, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 27, 28, 28, 27, 28, 28, 27, 27, 27, 81, 17, 17, 14, 14, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 27, 28, 28] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/842 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@](O)(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC000187504352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187504352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000187504352 none C[C@@](O)(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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] 1 hydrogens 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, 17, 29, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 31, 31, 29, 31, 31, 29, 29, 29, 87, 17, 17, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 29, 31, 31] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187504352 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 Building ZINC000187504352 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000187504352 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 841) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@](O)(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC000187504352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000187504352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000187504352 none C[C@@](O)(CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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] 1 hydrogens 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, 16, 27, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 27, 28, 28, 27, 28, 28, 27, 27, 27, 81, 17, 17, 14, 14, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 27, 28, 28] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 842) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@](O)(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1) `ZINC000187504352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000187504352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000187504352 none C[C@@](O)(CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccccc1 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 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, 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] 1 hydrogens 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, 17, 29, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 31, 31, 29, 31, 31, 29, 29, 29, 87, 17, 17, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 29, 31, 31] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000187504352 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000187504352 Building ZINC000342948975 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342948975 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/843 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CC2)cc1Cl) `ZINC000342948975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342948975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342948975 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 30, 30, 30, 30, 4, 4, 4, 10, 10, 10, 4, 4, 2, 12, 12, 30, 30, 30, 30, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/844 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CC2)cc1Cl) `ZINC000342948975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342948975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342948975 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 10, 4, 4, 2, 13, 13, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342948975 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 Building ZINC000342948975 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342948975 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 843) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CC2)cc1Cl) `ZINC000342948975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342948975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342948975 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 30, 30, 30, 30, 30, 30, 4, 4, 4, 10, 10, 10, 4, 4, 2, 12, 12, 30, 30, 30, 30, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 844) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CC2)cc1Cl) `ZINC000342948975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342948975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000342948975 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)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', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 10, 4, 4, 2, 13, 13, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342948975 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342948975 Building ZINC000342953224 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342953224 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/845 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000342953224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342953224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000342953224 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 15, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 30, 30, 30, 24, 24, 15, 15, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/846 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000342953224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342953224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000342953224 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 16, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 30, 30, 30, 25, 25, 16, 16, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342953224 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 Building ZINC000342953224 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000342953224 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 845) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000342953224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000342953224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000342953224 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 15, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 30, 30, 30, 24, 24, 15, 15, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 846) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F) `ZINC000342953224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000342953224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000342953224 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 16, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 30, 30, 30, 25, 25, 16, 16, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000342953224 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000342953224 Building ZINC000191132798 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191132798 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/847 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)cc1) `ZINC000191132798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191132798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191132798 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)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.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 13, 22, 26, 26, 21, 26, 26, 26, 38, 6, 6, 6, 6, 6, 6, 6, 4, 13, 13, 26, 26, 26, 38, 38, 38, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/848 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)cc1) `ZINC000191132798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191132798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191132798 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)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.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 13, 26, 26, 26, 21, 26, 26, 26, 38, 6, 6, 6, 6, 6, 6, 6, 4, 13, 13, 26, 26, 26, 38, 38, 38, 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]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191132798 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 Building ZINC000191132798 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191132798 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 847) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)cc1) `ZINC000191132798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191132798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191132798 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)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.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 13, 22, 26, 26, 21, 26, 26, 26, 38, 6, 6, 6, 6, 6, 6, 6, 4, 13, 13, 26, 26, 26, 38, 38, 38, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 848) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)cc1) `ZINC000191132798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191132798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191132798 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2c(Cl)cccc2OC)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.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 13, 26, 26, 26, 21, 26, 26, 26, 38, 6, 6, 6, 6, 6, 6, 6, 4, 13, 13, 26, 26, 26, 38, 38, 38, 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]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191132798 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191132798 Building ZINC000343008243 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343008243 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/849 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343008243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343008243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000343008243 none CC(C)(O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens 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, 20, 33, 33, 12, 5, 12, 30, 37, 37, 33, 37, 37, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 33, 33, 33, 33, 33, 99, 20, 20, 30, 30, 37, 37, 37, 37, 37, 2, 2, 2, 2] 150 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 340 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/850 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343008243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343008243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000343008243 none CC(C)(O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens 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, 20, 33, 33, 12, 6, 12, 28, 35, 35, 29, 35, 35, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 33, 33, 33, 33, 33, 99, 20, 20, 28, 28, 35, 35, 28, 35, 35, 2, 2, 2, 2] 150 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 336 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343008243 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 Building ZINC000343008243 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343008243 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 849) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343008243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343008243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000343008243 none CC(C)(O)CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens 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, 20, 33, 33, 12, 5, 12, 30, 37, 37, 33, 37, 37, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 33, 33, 33, 33, 33, 99, 20, 20, 30, 30, 37, 37, 37, 37, 37, 2, 2, 2, 2] 150 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 340 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 850) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343008243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343008243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000343008243 none CC(C)(O)CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens 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, 20, 33, 33, 12, 6, 12, 28, 35, 35, 29, 35, 35, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 33, 33, 33, 33, 33, 99, 20, 20, 28, 28, 35, 35, 28, 35, 35, 2, 2, 2, 2] 150 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 336 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343008243 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343008243 Building ZINC000343021624 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343021624 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/851 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Cl)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000343021624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343021624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000343021624 none Cc1ccc(Cl)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/852 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Cl)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000343021624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343021624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000343021624 none Cc1ccc(Cl)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343021624 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 Building ZINC000343021624 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343021624 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 851) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(Cl)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000343021624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343021624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000343021624 none Cc1ccc(Cl)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 852) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(Cl)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12) `ZINC000343021624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343021624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000343021624 none Cc1ccc(Cl)c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343021624 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343021624 Building ZINC000287491324 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287491324 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/853 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCOCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287491324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287491324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000287491324 none O=C(NCCCCOCc1ccccc1)[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', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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: [2, 1, 2, 2, 7, 8, 10, 15, 22, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 10, 15, 15, 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, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/854 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCOCc1ccccc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287491324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287491324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000287491324 none O=C(NCCCCOCc1ccccc1)[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', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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: [2, 1, 2, 2, 7, 8, 10, 18, 24, 49, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 10, 18, 18, 49, 49, 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, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287491324 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 Building ZINC000287491324 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287491324 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 853) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCCCOCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287491324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287491324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000287491324 none O=C(NCCCCOCc1ccccc1)[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', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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: [2, 1, 2, 2, 7, 8, 10, 15, 22, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 10, 15, 15, 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, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 854) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCCCCOCc1ccccc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287491324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287491324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000287491324 none O=C(NCCCCOCc1ccccc1)[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', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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: [2, 1, 2, 2, 7, 8, 10, 18, 24, 49, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 10, 18, 18, 49, 49, 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, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287491324 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287491324 Building ZINC000343109947 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343109947 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/855 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccn2)CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343109947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343109947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343109947 none O=C(NCC1(c2ccccn2)CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 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, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/856 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccccn2)CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343109947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343109947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343109947 none O=C(NCC1(c2ccccn2)CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343109947 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 Building ZINC000343109947 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343109947 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 855) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCC1(c2ccccn2)CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343109947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343109947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343109947 none O=C(NCC1(c2ccccn2)CCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 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, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 856) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(NCC1(c2ccccn2)CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343109947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343109947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343109947 none O=C(NCC1(c2ccccn2)CCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343109947 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343109947 Building ZINC000343142213 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343142213 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/857 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1OC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343142213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142213 none COc1ccccc1OC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 37, 16, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 16, 16, 11, 11, 11, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/858 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1OC[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343142213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142213 none COc1ccccc1OC[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 35, 17, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 49, 49, 49, 49, 17, 17, 12, 12, 12, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343142213 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 Building ZINC000343142213 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343142213 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 857) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1OC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343142213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142213 none COc1ccccc1OC[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 37, 16, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 16, 16, 11, 11, 11, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 858) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1OC[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343142213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142213 none COc1ccccc1OC[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 35, 17, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 49, 49, 49, 49, 17, 17, 12, 12, 12, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343142213 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142213 Building ZINC000343142635 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343142635 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/859 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1OC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343142635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142635 none COc1ccccc1OC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 34, 16, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 49, 49, 49, 49, 16, 16, 11, 11, 11, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/860 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1OC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343142635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142635 none COc1ccccc1OC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 50, 37, 17, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 17, 17, 12, 12, 12, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343142635 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 Building ZINC000343142635 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343142635 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 859) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1OC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343142635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142635 none COc1ccccc1OC[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 34, 16, 11, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 49, 49, 49, 49, 16, 16, 11, 11, 11, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 860) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccccc1OC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343142635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343142635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000343142635 none COc1ccccc1OC[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 50, 37, 17, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 17, 17, 12, 12, 12, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343142635 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343142635 Building ZINC000343198473 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343198473 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/861 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1) `ZINC000343198473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343198473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343198473 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 10, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/862 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1) `ZINC000343198473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343198473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343198473 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 31, 31, 31, 31, 31, 31, 31, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 10, 10, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343198473 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 Building ZINC000343198473 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343198473 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 861) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1) `ZINC000343198473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343198473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343198473 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 27, 27, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 10, 10, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 862) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1) `ZINC000343198473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343198473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343198473 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(C(F)(F)F)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 18, 31, 31, 31, 31, 31, 31, 31, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 10, 10, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343198473 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343198473 Building ZINC000343232649 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343232649 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/863 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343232649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232649 none C[C@@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 27, 27, 27, 27, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 27, 27, 27, 27, 27, 27, 27, 81, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/864 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343232649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232649 none C[C@@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 26, 26, 26, 26, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 78, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343232649 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 Building ZINC000343232649 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343232649 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 863) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343232649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232649 none C[C@@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 27, 27, 27, 27, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 27, 27, 27, 27, 27, 27, 27, 81, 11, 11, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 864) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343232649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232649 none C[C@@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 26, 26, 26, 26, 14, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 78, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343232649 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232649 Building ZINC000343232650 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343232650 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/865 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343232650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232650 none C[C@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 28, 28, 28, 28, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 84, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/866 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343232650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232650 none C[C@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 23, 26, 26, 26, 27, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 26, 26, 26, 26, 26, 27, 27, 81, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343232650 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 Building ZINC000343232650 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343232650 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 865) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343232650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232650 none C[C@H](CCO)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 27, 28, 28, 28, 28, 13, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 84, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 866) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1) `ZINC000343232650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343232650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000343232650 none C[C@H](CCO)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 23, 26, 26, 26, 27, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 26, 26, 26, 26, 26, 27, 27, 81, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343232650 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343232650 Building ZINC000343291216 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343291216 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/867 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343291216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343291216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343291216 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 4, 26, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 8, 26, 26, 26, 8, 8, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/868 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343291216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343291216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343291216 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 20, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 8, 8, 8, 28, 28, 28, 8, 8, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343291216 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 Building ZINC000343291216 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343291216 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 867) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343291216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343291216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343291216 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 4, 26, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 8, 26, 26, 26, 8, 8, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 868) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C) `ZINC000343291216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343291216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343291216 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 20, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 8, 8, 8, 28, 28, 28, 8, 8, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343291216 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343291216 Building ZINC000343314262 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343314262 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/869 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C) `ZINC000343314262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343314262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000343314262 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 24, 24, 24, 11, 13, 13, 13, 13, 13, 15, 15, 13, 13, 13, 4, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 13, 13, 13, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/870 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C) `ZINC000343314262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343314262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000343314262 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 22, 22, 22, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343314262 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 Building ZINC000343314262 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343314262 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 869) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C) `ZINC000343314262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343314262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000343314262 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 24, 24, 24, 11, 13, 13, 13, 13, 13, 15, 15, 13, 13, 13, 4, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 13, 13, 13, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 870) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C) `ZINC000343314262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343314262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000343314262 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cccc1N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 22, 22, 22, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343314262 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343314262 Building ZINC000287811619 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287811619 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/871 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000287811619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287811619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000287811619 none CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 1 hydrogens 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, 23, 18, 8, 3, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 20, 20, 27, 28, 28, 28, 27, 27, 27, 27, 27, 22, 23, 21, 21, 3, 2, 2, 4, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/872 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000287811619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287811619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000287811619 none CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 27, 21, 10, 4, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 28, 28, 28, 28, 30, 30, 30, 30, 30, 25, 27, 25, 25, 4, 3, 3, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287811619 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 Building ZINC000287811619 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000287811619 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 871) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000287811619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287811619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000287811619 none CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 1 hydrogens 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, 23, 18, 8, 3, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 20, 20, 27, 28, 28, 28, 27, 27, 27, 27, 27, 22, 23, 21, 21, 3, 2, 2, 4, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 872) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C) `ZINC000287811619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287811619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000287811619 none CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 27, 21, 10, 4, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 28, 28, 28, 28, 30, 30, 30, 30, 30, 25, 27, 25, 25, 4, 3, 3, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287811619 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287811619 Building ZINC000343334325 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343334325 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/873 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343334325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334325 none CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 12, 21, 21, 12, 12, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 23, 23, 23, 23, 23, 21, 21, 21, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/874 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343334325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334325 none CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 14, 27, 27, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 29, 29, 29, 29, 29, 27, 27, 27, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343334325 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 Building ZINC000343334325 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343334325 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 873) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343334325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334325 none CC[C@@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 12, 21, 21, 12, 12, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 23, 23, 23, 23, 23, 21, 21, 21, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 874) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343334325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334325 none CC[C@@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 14, 27, 27, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 29, 29, 29, 29, 29, 27, 27, 27, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343334325 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334325 Building ZINC000343334327 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343334327 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/875 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343334327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334327 none CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 13, 24, 24, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 28, 28, 28, 28, 28, 24, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/876 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343334327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334327 none CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 12, 24, 24, 12, 12, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 27, 27, 27, 27, 27, 24, 24, 24, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343334327 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 Building ZINC000343334327 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343334327 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 875) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343334327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334327 none CC[C@H](C)n1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 13, 24, 24, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 28, 28, 28, 28, 28, 24, 24, 24, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 876) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000343334327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343334327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000343334327 none CC[C@H](C)n1nc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 12, 24, 24, 12, 12, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 27, 27, 27, 27, 27, 24, 24, 24, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343334327 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343334327 Building ZINC000570279946 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279946 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/877 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279946 none O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 18, 18, 18, 18, 18, 18, 18, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 1, 1, 1, 4, 4, 4, 4, 4, 5, 18, 18, 18, 18, 18, 18, 40, 40, 40, 40, 18, 18, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/878 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279946 none O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 1, 1, 1, 4, 4, 4, 4, 4, 5, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279946 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 Building ZINC000570279946 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279946 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 877) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279946 none O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 18, 18, 18, 18, 18, 18, 18, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 1, 1, 1, 4, 4, 4, 4, 4, 5, 18, 18, 18, 18, 18, 18, 40, 40, 40, 40, 18, 18, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 878) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279946 none O=C(N[C@@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 1, 1, 1, 4, 4, 4, 4, 4, 5, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279946 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279946 Building ZINC000570279947 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279947 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/879 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279947 none O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 24, 24, 24, 24, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 1, 1, 1, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 24, 24, 40, 40, 40, 40, 24, 24, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/880 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279947 none O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 1, 1, 1, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279947 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 Building ZINC000570279947 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279947 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 879) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279947 none O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 24, 24, 24, 24, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 1, 1, 1, 3, 3, 3, 3, 3, 4, 24, 24, 24, 24, 24, 24, 40, 40, 40, 40, 24, 24, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 880) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279947 none O=C(N[C@H]1CCC[C@@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 1, 1, 1, 3, 3, 3, 3, 3, 5, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 25, 25, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279947 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279947 Building ZINC000570279948 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279948 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/881 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279948 none O=C(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 21, 21, 21, 21, 21, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 21, 1, 1, 1, 4, 4, 4, 4, 4, 5, 21, 21, 21, 21, 21, 21, 41, 41, 41, 41, 21, 21, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/882 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279948 none O=C(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 40, 40, 40, 40, 20, 20, 5, 5, 5] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279948 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 Building ZINC000570279948 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279948 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 881) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279948 none O=C(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 21, 21, 21, 21, 21, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 21, 1, 1, 1, 4, 4, 4, 4, 4, 5, 21, 21, 21, 21, 21, 21, 41, 41, 41, 41, 21, 21, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 882) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279948 none O=C(N[C@@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 40, 40, 40, 40, 40, 40, 40, 40, 40, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 40, 40, 40, 40, 20, 20, 5, 5, 5] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279948 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279948 Building ZINC000570279949 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279949 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/883 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279949 none O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 20, 20, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 37, 37, 37, 37, 20, 20, 5, 5, 5] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/884 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279949 none O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 6, 17, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 1, 1, 1, 3, 3, 3, 3, 3, 5, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 17, 17, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279949 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 Building ZINC000570279949 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000570279949 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 883) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000570279949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279949 none O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 20, 20, 20, 20, 20, 20, 20, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 37, 37, 37, 37, 20, 20, 5, 5, 5] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 884) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC000570279949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000570279949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000570279949 none O=C(N[C@H]1CCC[C@H](c2nc3ccccc3[nH]2)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 6, 17, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 1, 1, 1, 3, 3, 3, 3, 3, 5, 17, 17, 17, 17, 17, 17, 40, 40, 40, 40, 17, 17, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000570279949 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000570279949 Building ZINC000105860189 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860189 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/885 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860189 none Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 9, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/886 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860189 none Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 1, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 12, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860189 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 Building ZINC000105860189 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860189 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 885) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860189 none Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 9, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 886) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860189 none Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 1, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 12, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860189 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860189 Building ZINC000105860190 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860190 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/887 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860190 none Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 8, 1, 10, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 6, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/888 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860190 none Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 10, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860190 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 Building ZINC000105860190 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860190 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 887) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860190 none Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 8, 1, 10, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 14, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 6, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 888) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1) `ZINC000105860190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000105860190 none Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 10, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860190 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860190 Building ZINC000105860597 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860597 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/889 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860597 none Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 11, 1, 9, 1, 1, 1, 2, 2, 1, 2, 2, 2, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 21, 21, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/890 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860597 none Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 11, 1, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 18, 18, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860597 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 Building ZINC000105860597 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860597 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 889) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860597 none Cc1cnn([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 11, 1, 9, 1, 1, 1, 2, 2, 1, 2, 2, 2, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 21, 21, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 890) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860597 none Cc1cnn([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 11, 1, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 18, 18, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860597 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860597 Building ZINC000105860598 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860598 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/891 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860598 none Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/892 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860598 none Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 13, 1, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 20, 20, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860598 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 Building ZINC000105860598 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105860598 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 891) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105860598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860598 none Cc1cnn([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 892) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1) `ZINC000105860598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105860598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105860598 none Cc1cnn([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 13, 1, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 20, 20, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105860598 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105860598 Building ZINC000105862223 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105862223 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/893 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cnnc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000105862223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105862223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105862223 none CCn1cnnc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 36, 36, 36, 36, 36, 18, 18, 18, 18, 7, 2, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 50, 50, 50, 50, 50, 36, 18, 18, 18, 18, 18, 2, 2, 2, 2, 18, 18, 18, 18] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/894 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cnnc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000105862223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105862223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105862223 none CCn1cnnc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 31, 31, 31, 31, 31, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 50, 50, 31, 15, 15, 15, 15, 15, 3, 3, 3, 3, 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, 42]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105862223 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 Building ZINC000105862223 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105862223 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 893) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cnnc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000105862223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105862223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105862223 none CCn1cnnc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 36, 36, 36, 36, 36, 18, 18, 18, 18, 7, 2, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 50, 50, 50, 50, 50, 36, 18, 18, 18, 18, 18, 2, 2, 2, 2, 18, 18, 18, 18] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 894) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cnnc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000105862223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105862223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105862223 none CCn1cnnc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 31, 31, 31, 31, 31, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 50, 50, 31, 15, 15, 15, 15, 15, 3, 3, 3, 3, 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, 42]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000105862223 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000105862223 Building ZINC000287895365 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000287895365 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/895 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/896 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/897 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/897' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/898 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/898' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287895365 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 Building ZINC000287895365 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000287895365 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 895) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 896) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 897) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 898) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287895365 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 Building ZINC000287895365 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000287895365 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 895) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 896) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 897) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 898) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287895365 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 Building ZINC000287895365 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000287895365 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 895) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 896) grep: /scratch/xiaobo/25650/xaq-8058115.17/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@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 897) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 4, 2, 2] 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, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 898) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000287895365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000287895365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000287895365 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7] 1 hydrogens 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, 17, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 4, 2, 2] 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, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000287895365 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000287895365 Building ZINC000343410870 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000343410870 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/899 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/900 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/901 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/901' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/902 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/902' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343410870 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 Building ZINC000343410870 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000343410870 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 899) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 900) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 901) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 902) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343410870 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 Building ZINC000343410870 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000343410870 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 899) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 900) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 901) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 902) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343410870 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 Building ZINC000343410870 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000343410870 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 899) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 900) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `2' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 2 (index: 901) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 19, 19, 19, 19, 19, 50, 50, 23, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `3' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 3 (index: 902) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000343410870.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000343410870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000343410870 none O=C(N1CCCN(c2ccccc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 50, 50, 36, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343410870 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 3: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/3.* 2: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/2.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343410870 Building ZINC000343431453 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343431453 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/903 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343431453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431453 none CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 18, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 18, 18, 18, 18, 19, 19, 19, 14, 14, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/904 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343431453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431453 none CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 16, 21, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 8, 21, 21, 21, 21, 21, 21, 21, 16, 16, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343431453 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 Building ZINC000343431453 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343431453 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 903) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343431453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431453 none CS[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 18, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 18, 18, 18, 18, 19, 19, 19, 14, 14, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 904) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343431453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431453 none CS[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 16, 21, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 8, 21, 21, 21, 21, 21, 21, 21, 16, 16, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343431453 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431453 Building ZINC000343431456 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343431456 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/905 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343431456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431456 none CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 19, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 19, 19, 19, 19, 19, 19, 19, 15, 15, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/906 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343431456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431456 none CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 14, 15, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 19, 19, 19, 9, 15, 15, 15, 15, 16, 16, 16, 14, 14, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343431456 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 Building ZINC000343431456 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343431456 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 905) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343431456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431456 none CS[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 19, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 19, 19, 19, 19, 19, 19, 19, 15, 15, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 906) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C) `ZINC000343431456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343431456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000343431456 none CS[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 14, 15, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 19, 19, 19, 9, 15, 15, 15, 15, 16, 16, 16, 14, 14, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343431456 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343431456 Building ZINC000343438367 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343438367 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/907 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343438367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438367 none COCC[C@@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 11, 6, 3, 6, 6, 17, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 15, 15, 12, 12, 17, 17, 21, 21, 21, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/908 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343438367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438367 none COCC[C@@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 2, 5, 5, 12, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 12, 13, 10, 10, 12, 12, 16, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343438367 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 Building ZINC000343438367 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343438367 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 907) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCC[C@@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343438367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438367 none COCC[C@@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 11, 6, 3, 6, 6, 17, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 15, 15, 12, 12, 17, 17, 21, 21, 21, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 908) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCC[C@@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343438367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438367 none COCC[C@@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 2, 5, 5, 12, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 12, 13, 10, 10, 12, 12, 16, 16, 16, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343438367 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438367 Building ZINC000343438370 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343438370 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/909 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343438370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438370 none COCC[C@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 5, 2, 5, 5, 13, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 13, 12, 10, 10, 13, 13, 17, 17, 17, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/910 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343438370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438370 none COCC[C@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 11, 6, 3, 6, 6, 17, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 15, 15, 12, 12, 17, 17, 21, 21, 21, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343438370 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 Building ZINC000343438370 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343438370 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 909) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCC[C@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343438370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438370 none COCC[C@H](Cc1ccco1)NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 5, 2, 5, 5, 13, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 13, 12, 10, 10, 13, 13, 17, 17, 17, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 910) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCC[C@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343438370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343438370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000343438370 none COCC[C@H](Cc1ccco1)NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 11, 6, 3, 6, 6, 17, 21, 21, 21, 21, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 15, 15, 12, 12, 17, 17, 21, 21, 21, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343438370 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343438370 Building ZINC000188122549 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188122549 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/911 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC2COC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000188122549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188122549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000188122549 none O=C(Nc1ccc(OC2COC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 3, 3, 14, 34, 34, 34, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 34, 34, 34, 34, 34, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/912 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC2COC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000188122549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188122549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000188122549 none O=C(Nc1ccc(OC2COC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 5, 6, 19, 31, 31, 31, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 31, 31, 31, 31, 31, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000188122549 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 Building ZINC000188122549 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188122549 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 911) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1ccc(OC2COC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000188122549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188122549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000188122549 none O=C(Nc1ccc(OC2COC2)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 3, 3, 14, 34, 34, 34, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 34, 34, 34, 34, 34, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 912) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: O=C(Nc1ccc(OC2COC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000188122549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188122549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000188122549 none O=C(Nc1ccc(OC2COC2)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 5, 6, 19, 31, 31, 31, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 31, 31, 31, 31, 31, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000188122549 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188122549 Building ZINC000288014393 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288014393 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/913 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288014393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014393 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 50, 50, 50, 37, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 4, 4, 1, 2, 4, 4, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 10, 10, 10, 6, 4, 4, 8, 4, 4] 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, 45, 46]) total number of confs: 169 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/914 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288014393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014393 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 49, 49, 49, 34, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 34, 9, 9, 9, 5, 4, 4, 8, 4, 4] 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, 45, 46]) total number of confs: 174 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288014393 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 Building ZINC000288014393 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288014393 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 913) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288014393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014393 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 50, 50, 50, 37, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 4, 4, 1, 2, 4, 4, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 10, 10, 10, 6, 4, 4, 8, 4, 4] 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, 45, 46]) total number of confs: 169 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 914) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288014393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014393 none Cc1nn(C(C)(C)C)cc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 49, 49, 49, 34, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 34, 9, 9, 9, 5, 4, 4, 8, 4, 4] 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, 45, 46]) total number of confs: 174 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288014393 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014393 Building ZINC000288014394 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288014394 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/915 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288014394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014394 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 48, 48, 48, 35, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 35, 35, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 9, 9, 9, 5, 5, 5, 10, 5, 5] 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, 45, 46]) total number of confs: 170 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/916 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288014394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014394 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 50, 50, 50, 37, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 10, 10, 10, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288014394 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 Building ZINC000288014394 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288014394 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 915) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288014394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014394 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 48, 48, 48, 35, 9, 5, 9, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 35, 35, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 9, 9, 9, 5, 5, 5, 10, 5, 5] 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, 45, 46]) total number of confs: 170 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 916) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000288014394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288014394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000288014394 none Cc1nn(C(C)(C)C)cc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 5, 7, 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, 6, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 50, 50, 50, 37, 10, 6, 10, 10, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 10, 10, 10, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288014394 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288014394 Building ZINC000343531347 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343531347 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/917 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(C2CCOCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343531347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343531347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000343531347 none O=C(Nc1nc(C2CCOCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 14, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/918 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(C2CCOCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343531347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343531347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000343531347 none O=C(Nc1nc(C2CCOCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 14, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343531347 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 Building ZINC000343531347 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343531347 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 917) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(C2CCOCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343531347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343531347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000343531347 none O=C(Nc1nc(C2CCOCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 14, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 918) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(C2CCOCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000343531347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343531347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000343531347 none O=C(Nc1nc(C2CCOCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 14, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343531347 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343531347 Building ZINC000343576492 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343576492 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/919 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(C(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343576492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343576492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000343576492 none O=C(Nc1cnn(C(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 46, 46, 27, 1, 1, 1, 6, 6, 1, 6, 6, 6, 6, 27, 46, 27, 6, 6, 6, 6] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/920 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(C(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343576492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343576492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000343576492 none O=C(Nc1cnn(C(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 46, 46, 27, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 27, 46, 27, 6, 6, 6, 6] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343576492 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 Building ZINC000343576492 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343576492 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 919) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(C(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343576492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343576492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000343576492 none O=C(Nc1cnn(C(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 46, 46, 27, 1, 1, 1, 6, 6, 1, 6, 6, 6, 6, 27, 46, 27, 6, 6, 6, 6] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 920) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(C(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343576492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343576492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000343576492 none O=C(Nc1cnn(C(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 5, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 27, 27, 27, 27, 46, 46, 27, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 27, 46, 27, 6, 6, 6, 6] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343576492 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343576492 Building ZINC000343593495 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343593495 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/921 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343593495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343593495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343593495 none O=C(Nc1ccc(OCCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 2, 10, 13, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 13, 13, 28, 28, 28, 28, 84, 4, 4, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/922 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343593495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343593495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343593495 none O=C(Nc1ccc(OCCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 12, 12, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 12, 12, 28, 28, 28, 28, 84, 4, 4, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343593495 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 Building ZINC000343593495 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343593495 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 921) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343593495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343593495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343593495 none O=C(Nc1ccc(OCCCO)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 2, 10, 13, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 13, 13, 28, 28, 28, 28, 84, 4, 4, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 922) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000343593495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343593495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343593495 none O=C(Nc1ccc(OCCCO)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 4, 4, 12, 12, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 12, 12, 28, 28, 28, 28, 84, 4, 4, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343593495 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343593495 Building ZINC000288188525 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288188525 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/923 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C2) `ZINC000288188525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288188525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000288188525 none CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 1 hydrogens 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, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 44, 44, 9, 9, 9, 9, 9, 9, 9, 3, 3, 6, 3, 3, 9, 9] 100 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/924 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C2) `ZINC000288188525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288188525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000288188525 none CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 1 hydrogens 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, 36, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 50, 50, 50, 50, 50, 44, 44, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3, 10, 10] 100 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288188525 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 Building ZINC000288188525 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288188525 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 923) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C2) `ZINC000288188525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288188525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000288188525 none CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 1 hydrogens 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, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 44, 44, 9, 9, 9, 9, 9, 9, 9, 3, 3, 6, 3, 3, 9, 9] 100 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 924) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C2) `ZINC000288188525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288188525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000288188525 none CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7] 1 hydrogens 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, 36, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 50, 50, 50, 50, 50, 44, 44, 10, 10, 10, 10, 10, 10, 10, 3, 3, 6, 3, 3, 10, 10] 100 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288188525 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288188525 Building ZINC000343693009 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343693009 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/925 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000343693009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343693009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343693009 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 27, 27, 27, 24, 24, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/926 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000343693009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343693009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343693009 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 27, 27, 27, 23, 23, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343693009 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 Building ZINC000343693009 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343693009 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 925) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000343693009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343693009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343693009 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 27, 27, 27, 24, 24, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 926) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1) `ZINC000343693009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343693009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000343693009 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 27, 27, 27, 23, 23, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343693009 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343693009 Building ZINC000343737212 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343737212 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/927 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)cn1) `ZINC000343737212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343737212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000343737212 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 32, 32, 32, 32, 41, 41, 41, 41, 41, 32, 32, 32, 5, 5, 5, 5, 5, 5, 2, 14, 14, 32, 32, 41, 41, 41, 41, 41, 32, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/928 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)cn1) `ZINC000343737212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343737212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000343737212 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 21, 30, 41, 41, 41, 41, 41, 30, 30, 30, 5, 5, 5, 5, 5, 5, 2, 14, 14, 30, 30, 41, 41, 41, 41, 41, 30, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343737212 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 Building ZINC000343737212 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343737212 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 927) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)cn1) `ZINC000343737212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343737212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000343737212 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 32, 32, 32, 32, 41, 41, 41, 41, 41, 32, 32, 32, 5, 5, 5, 5, 5, 5, 2, 14, 14, 32, 32, 41, 41, 41, 41, 41, 32, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 928) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)cn1) `ZINC000343737212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343737212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000343737212 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccccc3)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 30, 30, 21, 30, 41, 41, 41, 41, 41, 30, 30, 30, 5, 5, 5, 5, 5, 5, 2, 14, 14, 30, 30, 41, 41, 41, 41, 41, 30, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343737212 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343737212 Building ZINC000343846190 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343846190 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/929 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343846190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846190 none CC(C)(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [48, 48, 48, 48, 44, 20, 47, 47, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 3, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 141, 20, 20, 4, 4, 4, 4, 4] 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: 360 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/930 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343846190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846190 none CC(C)(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [48, 48, 48, 48, 43, 19, 47, 47, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 141, 19, 19, 4, 4, 4, 4, 4] 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: 368 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343846190 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 Building ZINC000343846190 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343846190 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 929) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343846190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846190 none CC(C)(C)C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [48, 48, 48, 48, 44, 20, 47, 47, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 3, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 141, 20, 20, 4, 4, 4, 4, 4] 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: 360 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 930) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343846190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846190 none CC(C)(C)C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [48, 48, 48, 48, 43, 19, 47, 47, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 141, 19, 19, 4, 4, 4, 4, 4] 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: 368 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343846190 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846190 Building ZINC000343846191 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343846191 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/931 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343846191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846191 none CC(C)(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [48, 48, 48, 48, 47, 25, 48, 48, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 25, 25, 5, 4, 4, 4, 4] 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: 344 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/932 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343846191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846191 none CC(C)(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [46, 46, 46, 46, 45, 21, 46, 46, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 138, 21, 21, 5, 4, 4, 4, 4] 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: 338 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343846191 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 Building ZINC000343846191 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343846191 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 931) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343846191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846191 none CC(C)(C)C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [48, 48, 48, 48, 47, 25, 48, 48, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 25, 25, 5, 4, 4, 4, 4] 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: 344 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 932) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000343846191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343846191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000343846191 none CC(C)(C)C[C@H](O)CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 7, 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: [46, 46, 46, 46, 45, 21, 46, 46, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 138, 21, 21, 5, 4, 4, 4, 4] 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: 338 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343846191 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343846191 Building ZINC001137996126 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001137996126 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/933 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001137996126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001137996126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001137996126 none CCOC(=O)C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', '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, 5, 12, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 38, 19, 38, 19, 12, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 19, 19, 19, 19, 19, 12, 12, 4, 3, 1, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/934 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001137996126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001137996126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001137996126 none CCOC(=O)C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', '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, 5, 12, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 38, 15, 38, 13, 9, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 15, 15, 13, 13, 13, 9, 9, 4, 3, 1, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC001137996126 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 Building ZINC001137996126 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001137996126 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 933) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001137996126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001137996126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001137996126 none CCOC(=O)C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', '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, 5, 12, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 38, 19, 38, 19, 12, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 19, 19, 19, 19, 19, 12, 12, 4, 3, 1, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 934) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001137996126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001137996126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001137996126 none CCOC(=O)C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', '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, 5, 12, 1, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 38, 15, 38, 13, 9, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 15, 15, 13, 13, 13, 9, 9, 4, 3, 1, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC001137996126 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001137996126 Building ZINC000343916866 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343916866 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/935 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343916866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343916866 none Cc1noc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.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, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/936 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343916866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343916866 none Cc1noc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.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, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343916866 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 Building ZINC000343916866 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343916866 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 935) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1noc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343916866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343916866 none Cc1noc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.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, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 936) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1noc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)n1) `ZINC000343916866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343916866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000343916866 none Cc1noc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.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, 1, 8, 12, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 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, 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/25650/xaq-8058115.17/working/building/ZINC000343916866 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343916866 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343916866 Building ZINC000343941166 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941166 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/937 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941166 none CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 6, 20, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/938 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941166 none CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 7, 21, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 23, 23, 23, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343941166 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 Building ZINC000343941166 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941166 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 937) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941166 none CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 6, 20, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 20, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 938) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941166 none CC(C)(C)[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 7, 21, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 23, 23, 23, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343941166 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941166 Building ZINC000343941167 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941167 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/939 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941167 none CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 21, 21, 19, 19, 19, 7, 19, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 21, 21, 21, 11, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 5, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 19, 19, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/940 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941167 none CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 22, 18, 18, 18, 5, 18, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 18, 18, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 18, 18, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 18, 18, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343941167 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 Building ZINC000343941167 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941167 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 939) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941167 none CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 21, 21, 19, 19, 19, 7, 19, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 21, 21, 21, 11, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 5, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 19, 19, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 940) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941167 none CC(C)(C)[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 22, 18, 18, 18, 5, 18, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 18, 18, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 18, 18, 4, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 18, 18, 18, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343941167 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941167 Building ZINC000343941168 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941168 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/941 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941168 none CC(C)(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 23, 17, 17, 17, 6, 17, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/942 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941168 none CC(C)(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 22, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 4, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343941168 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 Building ZINC000343941168 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343941168 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 941) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343941168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941168 none CC(C)(C)[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 23, 17, 17, 17, 6, 17, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 942) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1) `ZINC000343941168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343941168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000343941168 none CC(C)(C)[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 22, 22, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 4, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343941168 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343941168 Building ZINC000343943603 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343943603 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/943 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1) `ZINC000343943603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343943603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943603 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 13, 2, 14, 1, 1, 1, 3, 3, 2, 2, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3, 31, 31] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/944 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1) `ZINC000343943603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343943603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943603 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 14, 2, 16, 1, 1, 1, 4, 4, 1, 2, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 35, 35] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343943603 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 Building ZINC000343943603 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343943603 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 943) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1) `ZINC000343943603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343943603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943603 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 13, 2, 14, 1, 1, 1, 3, 3, 2, 2, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3, 31, 31] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 944) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1) `ZINC000343943603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343943603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943603 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 14, 2, 16, 1, 1, 1, 4, 4, 1, 2, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 35, 35] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343943603 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943603 Building ZINC000343943604 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343943604 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/945 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1) `ZINC000343943604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343943604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943604 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 14, 2, 14, 1, 1, 1, 3, 3, 2, 2, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 32, 32] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/946 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1) `ZINC000343943604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343943604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943604 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 13, 2, 13, 1, 1, 1, 3, 3, 2, 2, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 30, 30] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343943604 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 Building ZINC000343943604 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000343943604 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 945) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1) `ZINC000343943604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000343943604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943604 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 14, 2, 14, 1, 1, 1, 3, 3, 2, 2, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 3, 32, 32] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 946) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1) `ZINC000343943604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000343943604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000343943604 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 13, 2, 13, 1, 1, 1, 3, 3, 2, 2, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 3, 30, 30] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000343943604 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000343943604 Building ZINC000191284598 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191284598 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/947 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191284598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284598 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 6, 26, 26, 26, 26, 26, 26, 52, 26, 26, 26, 7, 7] 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]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/948 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191284598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284598 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 54, 27, 27, 27, 10, 10] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191284598 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 Building ZINC000191284598 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191284598 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 947) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191284598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284598 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 7, 7, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 6, 26, 26, 26, 26, 26, 26, 52, 26, 26, 26, 7, 7] 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]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 948) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191284598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284598 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 54, 27, 27, 27, 10, 10] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191284598 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284598 Building ZINC000191284611 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191284611 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/949 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191284611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284611 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 54, 27, 27, 27, 10, 10] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/950 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191284611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284611 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 10, 6, 26, 26, 26, 26, 26, 26, 52, 26, 26, 26, 10, 10] 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]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191284611 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 Building ZINC000191284611 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000191284611 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 949) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N[C@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000191284611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284611 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 6, 27, 27, 27, 27, 27, 27, 54, 27, 27, 27, 10, 10] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 950) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)N[C@H]2CCCc3c(O)cccc32)cc1) `ZINC000191284611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000191284611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000191284611 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3c(O)cccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 10, 6, 26, 26, 26, 26, 26, 26, 52, 26, 26, 26, 10, 10] 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]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000191284611 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000191284611 Building ZINC000478664125 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478664125 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/951 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478664125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664125 none COc1ccc(OC)c([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 39, 12, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 28, 34, 34, 34, 28, 28, 39, 39, 39, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 28] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/952 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478664125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664125 none COc1ccc(OC)c([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 42, 15, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 34, 44, 44, 44, 34, 34, 42, 42, 42, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000478664125 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 Building ZINC000478664125 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478664125 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 951) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(OC)c([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478664125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664125 none COc1ccc(OC)c([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 28, 28, 39, 12, 12, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 28, 34, 34, 34, 28, 28, 39, 39, 39, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 28] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 952) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(OC)c([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478664125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664125 none COc1ccc(OC)c([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 42, 15, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 34, 44, 44, 44, 34, 34, 42, 42, 42, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000478664125 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664125 Building ZINC000478664126 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478664126 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/953 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478664126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664126 none COc1ccc(OC)c([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 30, 30, 30, 30, 30, 30, 41, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 30, 42, 42, 42, 30, 30, 41, 41, 41, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 30] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/954 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478664126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664126 none COc1ccc(OC)c([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 27, 37, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 27, 33, 33, 33, 27, 27, 37, 37, 37, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 27] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000478664126 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 Building ZINC000478664126 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000478664126 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 953) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(OC)c([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000478664126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664126 none COc1ccc(OC)c([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 30, 30, 30, 30, 30, 30, 41, 14, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 30, 42, 42, 42, 30, 30, 41, 41, 41, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 30] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 954) grep: /scratch/xiaobo/25650/xaq-8058115.17/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(OC)c([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1) `ZINC000478664126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000478664126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000478664126 none COc1ccc(OC)c([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cccn2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 27, 37, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 27, 33, 33, 33, 27, 27, 37, 37, 37, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 27] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000478664126 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000478664126 Building ZINC000344019720 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344019720 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/955 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000344019720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344019720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000344019720 none Cc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 27, 27, 20, 20, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/956 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000344019720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344019720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000344019720 none Cc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 19, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 27, 27, 19, 19, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344019720 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 Building ZINC000344019720 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344019720 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 955) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000344019720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344019720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000344019720 none Cc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 20, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 27, 27, 20, 20, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 956) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000344019720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344019720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000344019720 none Cc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 19, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 27, 27, 19, 19, 5, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344019720 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344019720 Building ZINC000344049999 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344049999 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/957 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1) `ZINC000344049999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344049999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000344049999 none Cc1cc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 30, 30] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/958 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1) `ZINC000344049999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344049999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000344049999 none Cc1cc2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344049999 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 Building ZINC000344049999 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344049999 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 957) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1) `ZINC000344049999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344049999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000344049999 none Cc1cc2cc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 30, 30] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 958) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1cc2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1) `ZINC000344049999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344049999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000344049999 none Cc1cc2cc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344049999 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344049999 Building ZINC000344118959 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344118959 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/959 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000344118959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344118959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344118959 none COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 20, 20, 20, 38, 38, 20, 38, 38, 20, 3, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 20, 37, 37, 37, 38, 38, 20, 38, 38, 20, 20, 4, 4, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/960 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000344118959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344118959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344118959 none COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 28, 28, 28, 49, 49, 28, 49, 49, 28, 3, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 28, 48, 48, 48, 49, 49, 28, 49, 49, 28, 28, 3, 3, 3, 3, 3, 3, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344118959 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 Building ZINC000344118959 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344118959 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 959) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000344118959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344118959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344118959 none COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 20, 20, 20, 38, 38, 20, 38, 38, 20, 3, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 20, 37, 37, 37, 38, 38, 20, 38, 38, 20, 20, 4, 4, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 960) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000344118959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344118959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344118959 none COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 28, 28, 28, 49, 49, 28, 49, 49, 28, 3, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 28, 48, 48, 48, 49, 49, 28, 49, 49, 28, 28, 3, 3, 3, 3, 3, 3, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344118959 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344118959 Building ZINC000344136143 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344136143 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/961 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1) `ZINC000344136143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344136143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000344136143 none CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 31, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 31, 31, 31, 31, 31, 31, 22, 22, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/962 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1) `ZINC000344136143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344136143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000344136143 none CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 34, 24, 24, 24, 24, 24, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 34, 34, 34, 34, 34, 34, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344136143 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 Building ZINC000344136143 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344136143 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 961) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1) `ZINC000344136143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344136143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000344136143 none CN(C)c1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 31, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 31, 31, 31, 31, 31, 31, 22, 22, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 962) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1) `ZINC000344136143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344136143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000344136143 none CN(C)c1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 34, 24, 24, 24, 24, 24, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 34, 34, 34, 34, 34, 34, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344136143 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344136143 Building ZINC000344147793 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344147793 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/963 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000344147793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344147793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000344147793 none COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 34, 34, 16, 34, 34, 16, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 16, 30, 30, 30, 34, 34, 16, 34, 34, 16, 16, 4, 4, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/964 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000344147793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344147793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000344147793 none COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 14, 14, 14, 30, 30, 14, 30, 30, 14, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 28, 28, 28, 30, 30, 14, 30, 30, 14, 14, 6, 6, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344147793 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 Building ZINC000344147793 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344147793 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 963) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000344147793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344147793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000344147793 none COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 34, 34, 16, 34, 34, 16, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 16, 30, 30, 30, 34, 34, 16, 34, 34, 16, 16, 4, 4, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 964) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000344147793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344147793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000344147793 none COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 14, 14, 14, 30, 30, 14, 30, 30, 14, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 28, 28, 28, 30, 30, 14, 30, 30, 14, 14, 6, 6, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344147793 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344147793 Building ZINC000344151367 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344151367 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/965 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344151367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151367 none CC[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 28, 28, 11, 2, 19, 1, 1, 1, 4, 4, 1, 4, 4, 4, 28, 28, 28, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/966 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344151367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151367 none CC[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 27, 27, 27, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344151367 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 Building ZINC000344151367 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344151367 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 965) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344151367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151367 none CC[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 28, 28, 11, 2, 19, 1, 1, 1, 4, 4, 1, 4, 4, 4, 28, 28, 28, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 966) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344151367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151367 none CC[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 27, 27, 27, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344151367 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151367 Building ZINC000344151368 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344151368 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/967 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344151368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151368 none CC[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 34, 34, 34, 10, 2, 14, 1, 1, 1, 5, 5, 1, 5, 5, 5, 34, 34, 34, 47, 47, 47, 47, 47, 34, 34, 34, 34, 34, 5, 5, 5, 5, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/968 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344151368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151368 none CC[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 28, 28, 10, 2, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 28, 28, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 5, 5, 5, 5, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344151368 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 Building ZINC000344151368 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344151368 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 967) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344151368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151368 none CC[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 34, 34, 34, 10, 2, 14, 1, 1, 1, 5, 5, 1, 5, 5, 5, 34, 34, 34, 47, 47, 47, 47, 47, 34, 34, 34, 34, 34, 5, 5, 5, 5, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 968) grep: /scratch/xiaobo/25650/xaq-8058115.17/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1) `ZINC000344151368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344151368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000344151368 none CC[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 28, 28, 10, 2, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 28, 28, 28, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 5, 5, 5, 5, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344151368 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344151368 Building ZINC000288888392 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888392 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/969 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/969' -> `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(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888392 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 20, 1, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 3, 3, 6, 3, 3, 35, 35, 50, 50, 50, 50] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/970 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/970' -> `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(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888392 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 30, 14, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 4, 4, 8, 4, 4, 30, 30, 48, 48, 48, 48] 100 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888392 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 Building ZINC000288888392 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888392 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 969) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888392 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 20, 1, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 3, 3, 6, 3, 3, 35, 35, 50, 50, 50, 50] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 970) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888392 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 30, 14, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 4, 4, 8, 4, 4, 30, 30, 48, 48, 48, 48] 100 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888392 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888392 Building ZINC000288888393 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888393 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/971 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/971' -> `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(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888393 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 30, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 45, 49, 49, 49, 30, 30, 30, 30, 30, 30, 5, 5, 10, 5, 5, 30, 30, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/972 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/972' -> `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(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888393 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 31, 15, 1, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 36, 36, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888393 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 Building ZINC000288888393 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888393 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 971) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888393 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 30, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 45, 49, 49, 49, 30, 30, 30, 30, 30, 30, 5, 5, 10, 5, 5, 30, 30, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 972) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000288888393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888393 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 31, 15, 1, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 36, 36, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 10, 5, 5, 31, 31, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888393 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888393 Building ZINC000288888394 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888394 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/973 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/973' -> `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(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888394 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 32, 13, 2, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 49, 49, 32, 32, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 10, 5, 5, 32, 32, 49, 49, 49, 49] 100 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/974 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/974' -> `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(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888394 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 11, 2, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 50, 50, 34, 34, 50, 50, 33, 33, 33, 33, 33, 33, 4, 4, 8, 4, 4, 33, 33, 50, 50, 50, 50] 100 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888394 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 Building ZINC000288888394 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888394 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 973) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888394 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 32, 13, 2, 15, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 49, 49, 32, 32, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 10, 5, 5, 32, 32, 49, 49, 49, 49] 100 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 974) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888394 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 11, 2, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 50, 50, 34, 34, 50, 50, 33, 33, 33, 33, 33, 33, 4, 4, 8, 4, 4, 33, 33, 50, 50, 50, 50] 100 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888394 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888394 Building ZINC000288888395 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888395 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/975 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/975' -> `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(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888395 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 32, 14, 1, 14, 1, 1, 1, 5, 5, 1, 2, 5, 5, 32, 32, 32, 32, 49, 49, 32, 49, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 10, 5, 5, 32, 32, 49, 49, 49, 49] 100 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/976 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/976' -> `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(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888395 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 49, 49, 29, 49, 49, 49, 29, 29, 29, 29, 29, 29, 5, 5, 10, 5, 5, 29, 29, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888395 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 Building ZINC000288888395 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000288888395 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 975) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000288888395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888395 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens 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, 32, 14, 1, 14, 1, 1, 1, 5, 5, 1, 2, 5, 5, 32, 32, 32, 32, 49, 49, 32, 49, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 10, 5, 5, 32, 32, 49, 49, 49, 49] 100 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 976) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000288888395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000288888395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000288888395 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 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, 9, 6, 8, 10, 11, 7, 7, 7, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 49, 49, 29, 49, 49, 49, 29, 29, 29, 29, 29, 29, 5, 5, 10, 5, 5, 29, 29, 49, 49, 49, 49] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000288888395 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000288888395 Building ZINC000344178196 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344178196 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/977 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000344178196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344178196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000344178196 none COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 14, 26, 26, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 22, 22, 22, 26, 26, 14, 26, 26, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/978 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000344178196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344178196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000344178196 none COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 25, 25, 12, 25, 25, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 23, 23, 23, 25, 25, 12, 25, 25, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344178196 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 Building ZINC000344178196 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344178196 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 977) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000344178196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344178196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000344178196 none COC1(c2ccccc2)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 14, 26, 26, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 22, 22, 22, 26, 26, 14, 26, 26, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 978) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000344178196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344178196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000344178196 none COC1(c2ccccc2)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.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'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 25, 25, 12, 25, 25, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 23, 23, 23, 25, 25, 12, 25, 25, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344178196 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344178196 Building ZINC000344254996 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344254996 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/979 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000344254996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344254996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000344254996 none COc1cc(OC)cc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 13, 17, 13, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 13, 16, 16, 16, 7, 17, 17, 17, 13, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/980 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000344254996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344254996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000344254996 none COc1cc(OC)cc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 4, 13, 13, 15, 13, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 13, 17, 17, 17, 4, 15, 15, 15, 13, 4, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344254996 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 Building ZINC000344254996 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344254996 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 979) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc(OC)cc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000344254996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344254996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000344254996 none COc1cc(OC)cc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 13, 17, 13, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 13, 16, 16, 16, 7, 17, 17, 17, 13, 4, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 980) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc(OC)cc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000344254996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344254996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000344254996 none COc1cc(OC)cc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 4, 13, 13, 15, 13, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 13, 17, 17, 17, 4, 15, 15, 15, 13, 4, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344254996 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344254996 Building ZINC000344257198 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344257198 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/981 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1) `ZINC000344257198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344257198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344257198 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 21, 21, 17, 21, 21, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 4, 10, 21, 21, 17, 21, 21, 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/982 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1) `ZINC000344257198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344257198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344257198 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 7, 7, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 21, 21, 9, 21, 21, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 4, 9, 21, 21, 21, 21, 21, 7] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344257198 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 Building ZINC000344257198 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344257198 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 981) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)n1cc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1) `ZINC000344257198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344257198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344257198 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 21, 21, 17, 21, 21, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 4, 10, 21, 21, 17, 21, 21, 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 982) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)n1cc([C@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1) `ZINC000344257198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344257198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344257198 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2c[nH]nc2c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 16, 7, 7, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 21, 21, 9, 21, 21, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 4, 9, 21, 21, 21, 21, 21, 7] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344257198 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344257198 Building ZINC000188965948 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188965948 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/983 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1c[nH]c2ccccc12)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000188965948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188965948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000188965948 none CCN(Cc1c[nH]c2ccccc12)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 13, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/984 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1c[nH]c2ccccc12)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000188965948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188965948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000188965948 none CCN(Cc1c[nH]c2ccccc12)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 13, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000188965948 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 Building ZINC000188965948 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188965948 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 983) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(Cc1c[nH]c2ccccc12)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000188965948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188965948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000188965948 none CCN(Cc1c[nH]c2ccccc12)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 13, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 984) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCN(Cc1c[nH]c2ccccc12)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000188965948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188965948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000188965948 none CCN(Cc1c[nH]c2ccccc12)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 13, 27, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000188965948 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000188965948 Building ZINC000344290319 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344290319 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/985 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000344290319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344290319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344290319 none COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 14, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 28, 28, 28, 24, 24, 14, 14, 8, 8, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/986 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000344290319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344290319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344290319 none COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 14, 8, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 27, 27, 27, 24, 24, 14, 14, 8, 2, 8, 8, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344290319 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 Building ZINC000344290319 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344290319 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 985) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000344290319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344290319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344290319 none COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 14, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 28, 28, 28, 24, 24, 14, 14, 8, 8, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 986) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000344290319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344290319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000344290319 none COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 14, 8, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 27, 27, 27, 24, 24, 14, 14, 8, 2, 8, 8, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344290319 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344290319 Building ZINC000344303238 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344303238 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/987 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/987' -> `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]2CSc3ccccc32)cn1) `ZINC000344303238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344303238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303238 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 4, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/988 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/988' -> `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]2CSc3ccccc32)cn1) `ZINC000344303238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344303238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303238 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 23, 11, 11, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 4, 13, 13, 13, 13, 13, 13, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344303238 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 Building ZINC000344303238 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344303238 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 987) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSc3ccccc32)cn1) `ZINC000344303238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344303238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303238 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 4, 13, 13, 13, 13, 13, 13, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 988) grep: /scratch/xiaobo/25650/xaq-8058115.17/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)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSc3ccccc32)cn1) `ZINC000344303238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344303238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303238 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 23, 11, 11, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 4, 13, 13, 13, 13, 13, 13, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344303238 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303238 Building ZINC000344303243 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344303243 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/989 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/989' -> `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]2CSc3ccccc32)cn1) `ZINC000344303243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344303243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303243 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 11, 11, 1, 1, 1, 1, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 4, 15, 15, 15, 15, 15, 15, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/990 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/990' -> `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]2CSc3ccccc32)cn1) `ZINC000344303243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344303243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303243 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 13, 13, 13, 13, 13, 13, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344303243 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 Building ZINC000344303243 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344303243 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 989) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSc3ccccc32)cn1) `ZINC000344303243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344303243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303243 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 11, 11, 1, 1, 1, 1, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 4, 15, 15, 15, 15, 15, 15, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 990) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CSc3ccccc32)cn1) `ZINC000344303243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344303243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000344303243 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CSc3ccccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 18, 18, 9, 9, 1, 1, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 13, 13, 13, 13, 13, 13, 9] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344303243 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344303243 Building ZINC000344320321 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344320321 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/991 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC000344320321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344320321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000344320321 none Cc1ccc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 38, 45, 45, 45, 45, 45, 45, 45, 38, 38, 38, 11, 11, 2, 4, 4, 4, 4, 4, 38, 45, 45] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/992 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC000344320321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344320321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000344320321 none Cc1ccc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 36, 36, 36, 36, 36, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 36, 43, 43, 43, 43, 43, 43, 43, 36, 36, 36, 11, 11, 2, 4, 4, 4, 4, 4, 36, 43, 43] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344320321 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 Building ZINC000344320321 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344320321 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 991) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC000344320321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344320321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000344320321 none Cc1ccc(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 38, 45, 45, 45, 45, 45, 45, 45, 38, 38, 38, 11, 11, 2, 4, 4, 4, 4, 4, 38, 45, 45] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 992) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: Cc1ccc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC000344320321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344320321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000344320321 none Cc1ccc(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 36, 36, 36, 36, 36, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 36, 43, 43, 43, 43, 43, 43, 43, 36, 36, 36, 11, 11, 2, 4, 4, 4, 4, 4, 36, 43, 43] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344320321 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344320321 Building ZINC000289135409 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289135409 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/993 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289135409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289135409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000289135409 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 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, 6, 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] 1 hydrogens 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, 3, 6, 22, 47, 50, 50, 47, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/994 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289135409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289135409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000289135409 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 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, 6, 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] 1 hydrogens 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, 3, 6, 23, 48, 50, 50, 48, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000289135409 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 Building ZINC000289135409 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000289135409 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 993) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289135409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000289135409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000289135409 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 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, 6, 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] 1 hydrogens 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, 3, 6, 22, 47, 50, 50, 47, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 994) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000289135409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000289135409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000289135409 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 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, 6, 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] 1 hydrogens 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, 3, 6, 23, 48, 50, 50, 48, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000289135409 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000289135409 Building ZINC001135054038 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001135054038 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/995 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1) `ZINC001135054038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001135054038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001135054038 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 27, 27, 27, 27, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/996 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1) `ZINC001135054038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001135054038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001135054038 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 26, 26, 26, 26, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC001135054038 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 Building ZINC001135054038 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001135054038 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 995) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1) `ZINC001135054038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001135054038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001135054038 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 27, 27, 27, 27, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 996) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1) `ZINC001135054038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001135054038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001135054038 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ncc(c3cccc(F)c3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 26, 26, 26, 26, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC001135054038 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC001135054038 Building ZINC000344434169 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344434169 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/997 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1) `ZINC000344434169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344434169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344434169 none COCc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 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] 0 hydrogens 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, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 22, 22, 22, 12, 34, 34, 34, 34, 34, 12, 2, 2, 2, 2, 2, 12, 22, 22, 22, 12] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/998 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1) `ZINC000344434169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344434169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344434169 none COCc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 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] 0 hydrogens 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, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 22, 22, 22, 12, 34, 34, 34, 34, 34, 12, 2, 2, 2, 2, 2, 12, 22, 22, 22, 12] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344434169 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 Building ZINC000344434169 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344434169 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 997) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1) `ZINC000344434169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344434169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344434169 none COCc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 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] 0 hydrogens 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, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 22, 22, 22, 12, 34, 34, 34, 34, 34, 12, 2, 2, 2, 2, 2, 12, 22, 22, 22, 12] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 998) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COCc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1) `ZINC000344434169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344434169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344434169 none COCc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc(C(=O)OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 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] 0 hydrogens 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, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 22, 22, 22, 12, 34, 34, 34, 34, 34, 12, 2, 2, 2, 2, 2, 12, 22, 22, 22, 12] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344434169 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344434169 Building ZINC000344461066 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344461066 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/999 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/999' -> `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)cc1F) `ZINC000344461066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344461066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344461066 none COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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', 'F', 'H', 'H', '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, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 11, 11, 11, 22, 22, 22, 11, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/25650/xaq-8058115.17/working/3D/1000 `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/1000' -> `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)cc1F) `ZINC000344461066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344461066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344461066 none COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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', 'F', 'H', 'H', '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, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 8, 9, 9, 9, 20, 20, 20, 9, 3, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344461066 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 Building ZINC000344461066 mkdir: created directory `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000344461066 mkdir: created directory `0' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/0 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 0 (index: 999) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000344461066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000344461066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344461066 none COc1cc(F)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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', 'F', 'H', 'H', '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, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 11, 11, 11, 22, 22, 22, 11, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 mkdir: created directory `1' /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/1 /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Protomer 1 (index: 1000) grep: /scratch/xiaobo/25650/xaq-8058115.17/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: COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F) `ZINC000344461066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000344461066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000344461066 none COc1cc(F)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1F 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', 'F', 'H', 'H', '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, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 8, 9, 9, 9, 20, 20, 20, 9, 3, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Finished preparing ZINC000344461066 Recording results /scratch/xiaobo/25650/xaq-8058115.17/working /scratch/xiaobo/25650/xaq-8058115.17 Appending to /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.* 1: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/1.* 0: /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066/0.* Removing working files in /scratch/xiaobo/25650/xaq-8058115.17/working/building/ZINC000344461066 /scratch/xiaobo/25650/xaq-8058115.17 Compressing combined databse files /scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/25650/xaq-8058115.17/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/25650/xaq-8058115.17/working/3D/1001' removed directory: `/scratch/xiaobo/25650/xaq-8058115.17/working/3D' rmdir: removing directory, `/scratch/xiaobo/25650/xaq-8058115.17/working/building' rmdir: removing directory, `/scratch/xiaobo/25650/xaq-8058115.17/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/25650/xaq-8058115.17' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xaq' `/scratch/xiaobo/25650/xaq-8058115.17/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xaq/finished' `/scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xaq/finished/xaq.db2.gz' removed `/scratch/xiaobo/25650/xaq-8058115.17/finished/xaq.db2.gz' removed directory: `/scratch/xiaobo/25650/xaq-8058115.17/finished' removed directory: `/scratch/xiaobo/25650/xaq-8058115.17'